Comprehensive Analysis of Gene Expression Profiles of Sepsis-Induced Multiorgan Failure Identified Its Valuable Biomarkers.

Abstract:

:Sepsis is an inflammatory-related disease, and severe sepsis would induce multiorgan dysfunction, which is the most common cause of death of patients in noncoronary intensive care units. Progression of novel therapeutic strategies has proven to be of little impact on the mortality of severe sepsis, and unfortunately, its mechanisms still remain poorly understood. In this study, we analyzed gene expression profiles of severe sepsis with failure of lung, kidney, and liver for the identification of potential biomarkers. We first downloaded the gene expression profiles from the Gene Expression Omnibus and performed preprocessing of raw microarray data sets and identification of differential expression genes (DEGs) through the R programming software; then, significantly enriched functions of DEGs in lung, kidney, and liver failure sepsis samples were obtained from the Database for Annotation, Visualization, and Integrated Discovery; finally, protein-protein interaction network was constructed for DEGs based on the STRING database, and network modules were also obtained through the MCODE cluster method. As a result, lung failure sepsis has the highest number of DEGs of 859, whereas the number of DEGs in kidney and liver failure sepsis samples is 178 and 175, respectively. In addition, 17 overlaps were obtained among the three lists of DEGs. Biological processes related to immune and inflammatory response were found to be significantly enriched in DEGs. Network and module analysis identified four gene clusters in which all or most of genes were upregulated. The expression changes of Icam1 and Socs3 were further validated through quantitative PCR analysis. This study should shed light on the development of sepsis and provide potential therapeutic targets for sepsis-induced multiorgan failure.

journal_name

DNA Cell Biol

journal_title

DNA and cell biology

authors

Wang Y,Yin X,Yang F

doi

10.1089/dna.2017.3944

subject

Has Abstract

pub_date

2018-02-01 00:00:00

pages

90-98

issue

2

eissn

1044-5498

issn

1557-7430

journal_volume

37

pub_type

杂志文章
  • A human gene encoding a putative basic helix-loop-helix phosphoprotein whose mRNA increases rapidly in cycloheximide-treated blood mononuclear cells.

    abstract::G0S8 is a member of a set of putative G0/G1 switch regulatory genes (G0S genes) selected by screening cDNA libraries prepared from blood mononuclear cells cultured for 2 hr with lectin and cycloheximide. Comparison of a full-length cDNA sequence with the corresponding genomic sequence reveals an open reading frame of ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1994.13.125

    authors: Siderovski DP,Heximer SP,Forsdyke DR

    更新日期:1994-02-01 00:00:00

  • Induction of HLA class II molecules on human T cells: relationship to immunoregulation and the pathogenesis of AIDS.

    abstract::Human T cells express HLA class II molecules upon activation. The factors that regulate the induction of expression of these molecules are for the most part unknown. Here we report preliminary results indicating that tumor necrosis factor-alpha (TNF-alpha) regulates the induction of cell-surface HLA-DR, DO, and DP mol...

    journal_title:DNA and cell biology

    pub_type: 杂志文章,评审

    doi:10.1089/dna.1992.11.265

    authors: Kamoun M,Zerva L,Sloan S,Zmijewski C,Monos D,Trinchieri G

    更新日期:1992-04-01 00:00:00

  • In silico and in vitro characterization of mGBP4 splice variants.

    abstract::In a systematic approach to identify interferon-gamma (IFN-gamma)-regulated host effector molecules, we found several members of the 65 kDa guanylate-binding proteins (GBPs) highly upregulated. During extensive characterization of these guanosine triphosphatases (GTPases), we identified discrepancies between the clone...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2007.0637

    authors: Konermann C,Kresse A,Beuter-Gunia C,Würthner J,Degrandi D,Pfeffer K,Beer S

    更新日期:2007-12-01 00:00:00

  • Characterization of a cDNA encoding rat sterol carrier protein2.

    abstract::Sterol carrier protein2 (SCP2) is a 13.2-kD protein that is thought to be involved in the intracellular transport of cholesterol. Using synthetic oligonucleotides based on the protein sequence of SCP2, a clone (SP43) was isolated from a rat liver cDNA library. The DNA sequence revealed that the cDNA could encode a pol...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1990.9.159

    authors: Billheimer JT,Strehl LL,Davis GL,Strauss JF 3rd,Davis LG

    更新日期:1990-04-01 00:00:00

  • Chicken ovalbumin upstream promoter-transcription factor, hepatocyte nuclear factor 3, and CCAAT/enhancer binding protein control the far-upstream enhancer of the rat alpha-fetoprotein gene.

    abstract::We have further characterized the most distal of the three alpha-fetoprotein (AFP) enhancers required for expression of the AFP gene in fetal hepatocytes and yolk sac endodermal cells. Almost total rat AFP enhancer 3 (E3) activity is driven by a 160-bp fragment at -6 kb containing three target regions for nuclear prot...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1996.15.1063

    authors: Thomassin H,Bois-Joyeux B,Delille R,Ikonomova R,Danan JL

    更新日期:1996-12-01 00:00:00

  • In Silico Detection and Characterization of microRNAs and Their Target Genes in microRNA Microarray Datasets from Patients with Systemic Sclerosis-Interstitial Lung Disease.

    abstract::Interstitial lung disease (ILD) is the main reason of death in patients with systemic sclerosis (SSc). The potential microRNA (miRNA)-messenger RNA (mRNA) interaction networks of SSc-ILD from a systematic biological perspective are unclear. To characterize differentially expressed miRNAs (DE-miRNAs) and differentially...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2019.4780

    authors: He Y,Liu H,Wang S,Chen Y

    更新日期:2019-09-01 00:00:00

  • Gene set enrichment analysis reveals several globally affected pathways due to SKI-1/S1P inhibition in HepG2 cells.

    abstract::Sterol regulatory element-binding proteins (SREBPs) are transcription factors governing transcription of genes related to cholesterol and fatty acid metabolism. To become active, SREBPs must undergo a proteolytic cleavage to allow an active NH(2)-terminal segment to translocate into the nucleus. SKI-1/S1P is the first...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2007.0624

    authors: De Windt A,Rai M,Bernier L,Thelen K,Soini J,Lefebvre C,Chintawar S,Lavigne J,Saarinen L,Kytömäki L,Munzer JS,Lütjohann D,Pandolfo M,Davignon J,Seidah NG,Laaksonen R

    更新日期:2007-11-01 00:00:00

  • Expression of the proto-oncogene Axl in renal cell carcinoma.

    abstract::In this investigation, we examined the role of the Axl proto-oncogene in renal cell carcinoma (RCC). Axl is a tyrosine kinase receptor implicated in myeloid leukogenesis, and has been found to be overexpressed in lung cancers and breast cancers. Axl has been described to act as a mitogenic factor along with its ligand...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/10445490360708946

    authors: Chung BI,Malkowicz SB,Nguyen TB,Libertino JA,McGarvey TW

    更新日期:2003-08-01 00:00:00

  • Characterization of genetic variation in the Forkhead box class O3 gene (FOXO3) in sheep.

    abstract::FOXO3 is a member of the Forkhead box class O (FOXO) transcription factor family that modulates the transcription of target genes in a variety of cellular functions in lower animals to mammals. It has been implicated in the attenuation of insulin-signaling pathways, including having a potential role in lifespan contro...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2010.1193

    authors: Byun SO,Zhou H,Hickford JG

    更新日期:2011-07-01 00:00:00

  • Cytosine Methylation of Isoflavone Synthase Gene in the Genic Region Positively Regulates Its Expression and Isoflavone Biosynthesis in Soybean Seeds.

    abstract::Plants, being sessile organisms, have evolved several dynamic mechanisms of gene regulation. Epigenetic modification especially cytosine methylation and demethylation actively regulates the expression of genes. To understand the role of cytosine methylation during isoflavonoid biosynthesis and accumulation, we perform...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2018.4584

    authors: Gupta OP,Dahuja A,Sachdev A,Jain PK,Kumari S,T V,Praveen S

    更新日期:2019-06-01 00:00:00

  • The Wilms' tumor gene 1 (WT1) induces expression of the N-myc downstream regulated gene 2 (NDRG2).

    abstract::The Wilms' tumor gene 1 (WT1) protein is a transcriptional regulator that is highly expressed in immature hematopoietic progenitor cells and in the majority of patients with acute and chronic myeloid leukemia. However, it is still unclear how WT1 exerts its function(s) in hematopoietic cells. The aim of this work was ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2007.0586

    authors: Svensson E,Vidovic K,Olofsson T,Vallon-Christersson J,Borg A,Gullberg U

    更新日期:2007-08-01 00:00:00

  • ALDH2 rs671 Polymorphism and coronary heart disease risk among Asian populations: a meta-analysis and meta-regression.

    abstract::Mitochondrial aldehyde dehydrogenase-2 (ALDH2) is the principal enzyme involved in alcohol metabolism in humans. Emerging evidence has shown that the common rs671 G>A (Glu504Lys) polymorphism in the ALDH2 gene might play a critical role in increasing the susceptibility to coronary heart disease (CHD), including myocar...

    journal_title:DNA and cell biology

    pub_type: 杂志文章,meta分析

    doi:10.1089/dna.2013.1995

    authors: Wang Q,Zhou S,Wang L,Lei M,Wang Y,Miao C,Jin Y

    更新日期:2013-07-01 00:00:00

  • MMP7 -181G allele is a low-penetrant risk factor for cancer development in East Asians.

    abstract::Matrix metalloproteinase-7 (MMP-7) is a small secreted proteolytic enzyme with broad substrate specificity. Its expression is associated with tumor invasion, metastasis, and survival for a number of cancers. However, data from published studies with individually low statistical power are conflicting. Here, we performe...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2011.1416

    authors: Yuan-Yuan M,Li-Feng Z,Li-Jie Z

    更新日期:2012-05-01 00:00:00

  • Transforming growth factor-B1 and matrix metalloproteinase-7 promoter variants induce risk for Helicobacter pylori-associated gastric precancerous lesions.

    abstract::The expression of growth factors, proteolytic enzymes, fibrogenic factors, and cytokines is altered in the Helicobacter pylori-infected gastric mucosa. Therefore, we aimed to evaluate the association of functional promoter variants of transforming growth factor (TGF)-B1 and matrix metalloproteinase (MMP)-7 genes with ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2008.0842

    authors: Achyut BR,Ghoshal UC,Moorchung N,Mittal B

    更新日期:2009-06-01 00:00:00

  • Selective binding of specific mouse genomic DNA fragments by mouse vimentin filaments in vitro.

    abstract::Mouse vimentin intermediate filaments (IFs) reconstituted in vitro were analyzed for their capacity to select certain DNA sequences from a mixture of about 500-bp-long fragments of total mouse genomic DNA. The fragments preferentially bound by the IFs and enriched by several cycles of affinity binding and polymerase c...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1996.15.209

    authors: Wang X,Tolstonog G,Shoeman RL,Traub P

    更新日期:1996-03-01 00:00:00

  • Closely related genes encode developmental and tissue isoforms of porcine cytochrome P450 aromatase.

    abstract::We examined the chromosomal basis for the synthesis of tissue (ovary, endometrium/placenta, and peri-implantation blastocyst) isoforms of cytochrome P450 aromatase in the pig. DNA fragments derived from three distinct porcine aromatase chromosomal genes were cloned and characterized. The porcine type III aromatase gen...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1997.16.769

    authors: Choi I,Troyer DL,Cornwell DL,Kirby-Dobbels KR,Collante WR,Simmen FA

    更新日期:1997-06-01 00:00:00

  • Simulated microgravity contributes to autophagy induction by regulating AMP-activated protein kinase.

    abstract::Exposure to microgravity is supposed to affect almost all biological systems, and we speculated that microgravity is potentially involved in autophagy regulation. A clinostat was used to simulate microgravity, and HEK293 cells that stably express GFP-LC3 were used for sensitive monitoring of autophagy induction. The c...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2013.2089

    authors: Ryu HW,Choi SH,Namkoong S,Jang IS,Seo DH,Choi I,Kim HS,Park J

    更新日期:2014-03-01 00:00:00

  • Evaluation of genetic immunization adjuvants to improve the effectiveness of a human immunodeficiency virus type 2 (HIV-2) envelope DNA vaccine.

    abstract::In an effort to develop a more effective genetic immunization strategy for HIV, we developed an HIV-2 env DNA vaccine and evaluated three adjuvant formulations. The gp140 gene from HIV-2(UC2 )was synthesized using mammalian codons and cloned into a plasmid vector that expresses eukaryotic genes at high levels. We foun...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/104454904322759911

    authors: Locher CP,Witt SA,Ashlock BM,Levy JA

    更新日期:2004-02-01 00:00:00

  • The human AKNA gene expresses multiple transcripts and protein isoforms as a result of alternative promoter usage, splicing, and polyadenylation.

    abstract::We previously showed that the human AKNA gene encodes an AT-hook transcription factor that regulates the expression of costimulatory cell surface molecules on lymphocytes. However, AKNA cDNA probes hybridize with multiple transcripts, suggesting either the existence of other homologous genes or a complex regulation op...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2005.24.325

    authors: Sims-Mourtada JC,Bruce S,McKeller MR,Rangel R,Guzman-Rojas L,Cain K,Lopez C,Zimonjic DB,Popescu NC,Gordon J,Wilkinson MF,Martinez-Valdez H

    更新日期:2005-05-01 00:00:00

  • Fidelity and predominant mutations produced by deep vent wild-type and exonuclease-deficient DNA polymerases during in vitro DNA amplification.

    abstract::Denaturing gradient gel electrophoresis (DGGE) was used to examine error rates and mutations induced by native (wt) and exonuclease-deficient (exo-) Deep Vent DNA polymerases during DNA amplification by polymerase chain reaction (PCR), in the presence or absence of the T4 bacteriophage gene 32 protein (gp32).gp32 was ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1996.15.589

    authors: Huang H,Keohavong P

    更新日期:1996-07-01 00:00:00

  • Glucose response elements in a gene that codes for 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.

    abstract::We have shown previously that rat hepatoma FTO-2B cells express two mRNAs, called F (fetal) and L (liver), from distinct promoters of the same gene coding for 6-phosphofructo-2-kinase (PFK-2). This enzyme catalyzes the synthesis of fructose 2,6-bisphosphate, an allosteric stimulator of glycolysis. We have now found th...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1997.16.1075

    authors: Dupriez VJ,Rousseau GG

    更新日期:1997-09-01 00:00:00

  • Bacterial expression and characterization of recombinant biologically active anti-tyrosine kinase receptor antibody forms.

    abstract::Homomeric and heteromeric interactions among cell-surface tyrosine kinase receptors belonging to the ErbB family lead to intracellular signaling cascades which are involved in cell activation, cytoskeletal interactions, and cellular transformation leading to neoplasia. Monoclonal antibodies which specifically bind to ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1998.17.1031

    authors: Peterson NC,Greene MI

    更新日期:1998-12-01 00:00:00

  • Complete structure and expression of the rat alpha B-crystallin gene.

    abstract::alpha B-Crystallin, a member of the small heat shock family of proteins, is synthesized as a component of various developmental programs, in response to stress and in a number of pathological states. We have determined the complete structure of the alpha B-crystallin gene (6,806 bp encompassing 2,299 bp upstream from ...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1994.13.651

    authors: Srinivasan AN,Bhat SP

    更新日期:1994-06-01 00:00:00

  • Transfer RNA binding to human serum albumin: a model for protein-RNA interaction.

    abstract::Protein-RNA complexation is essential in cell biological functions. Transfer RNAs are bound to aminoacyl-tRNA synthetases for the translation of the genetic code during protein synthesis, while ribonucleoproteins bind RNA in posttranscriptional regulation of gene expression. A recent report showed the interacton of hu...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2006.25.393

    authors: Malonga H,Neault JF,Tajmir-Riahi HA

    更新日期:2006-07-01 00:00:00

  • Bioinformatics Analysis of the Core Genes Related to Lupus Nephritis Through a Network and Pathway-Based Approach.

    abstract::In this study, we explored the genes genetically associated with lupus nephritis (LN), and their function by bioinformatics analysis. We collected genes potentially associated with LN from National Center for Biotechnology Information Center (NCBI-Gene) and Online Mendelian Inheritance in Man (OMIM) databases. The maj...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2019.4631

    authors: Sun G,Zhu P,Dai Y,Chen W

    更新日期:2019-07-01 00:00:00

  • The final moments of misfolded proteins en route to the proteasome.

    abstract::Protein homeostasis in the endoplasmic reticulum (ER) in eukaryotic cells is maintained by a conserved quality control system named ER-associated degradation (ERAD). The ERAD system retains misfolded or unassembled polypeptides in the ER, retrotranslocates them into the cytosol for degradation by the ubiquitin proteas...

    journal_title:DNA and cell biology

    pub_type: 杂志文章,评审

    doi:10.1089/dna.2014.2452

    authors: Zhang T,Ye Y

    更新日期:2014-08-01 00:00:00

  • Enhancement of the TCRζ expression, polyclonal expansion, and activation of t cells from patients with acute myeloid leukemia after IL-2, IL-7, and IL-12 induction.

    abstract::Defective T cell receptor (TCR) signaling resulting in lower T cell function plays a crucial role in the pathogenesis of T cell immunodeficiency in leukemia. Previous studies have indicated that lower TCRζ levels are a common characteristic of patients with leukemia, and upregulating TCRζ could partially recover T cel...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2015.2810

    authors: Shi L,Chen S,Zha X,Xu Y,Xu L,Yang L,Lu Y,Zhu K,Li Y

    更新日期:2015-07-01 00:00:00

  • Characterization of murine middle repetitive DNA.

    abstract::We have characterized four sequences from a small library containing a subset of the repetitive families of the mouse. Each clone has a repetition frequency of less than 1,100 copies per genome and each clone represents a unique family of middle repetitive DNA. One clone (pMR111) shares homology with mouse intracister...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1993.12.319

    authors: Adiletta DC,Elliott RW,Woodworth ME

    更新日期:1993-05-01 00:00:00

  • SLC34A2 Regulates the Proliferation, Migration, and Invasion of Human Osteosarcoma Cells Through PTEN/PI3K/AKT Signaling.

    abstract::Osteosarcoma (OS) is a bone malignancy with high incidence. The underlying molecular mechanisms that are associated with the development of OS need further investigation. In this study, we showed that SLC34A2, a member of the solute carrier gene family, was significantly downregulated in OS patients and cell lines. Ov...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.2017.3750

    authors: Liu X,Zhou X,Xu H,He Z,Shi X,Wu S

    更新日期:2017-09-01 00:00:00

  • Synchronous block in DNA synthesis initiation with change in chromatin topology mediated by VP16.

    abstract::The impact of chromatin topology on the DNA synthetic process was studied in the human squamous-cell carcinoma cell line SQ-20B. A 1-h exposure < or = 10 microM VP16 produced an increase in DNA supercoil tension, measured by recording laser light scatter from salt-extracted nuclei. This change was precisely paralleled...

    journal_title:DNA and cell biology

    pub_type: 杂志文章

    doi:10.1089/dna.1998.17.613

    authors: Narayana A,Khodarev N,Walter S,Vaughan AT

    更新日期:1998-07-01 00:00:00