scholarly journals Coding and non-coding RNAs transcribed at the RORA locus (ROR𝛂) are differentially expressed in the whole blood of sepsis patients.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Expression Analysis ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Differentially Expressed ◽  
Blood Gene Expression ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Sepsis is a leading cause of mortality (1). We mined published datasets from the whole blood of patients with sepsis to identify differentially expressed genes in the septic state (2, 3). We found changes in RORA expression as among the most significant quantitative differences in sepsis whole blood gene expression. Analysis of a separate dataset (4) demonstrated significant repression of a long non-coding RNA produced at the RORA locus in the blood of patients with sepsis.

scholarly journals Changes in gene expression at the CD160 locus in the whole blood of sepsis patients.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Expression Analysis ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Differentially Expressed ◽  
Blood Gene Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Sepsis is a leading cause of mortality (1). We mined published datasets from the whole blood of patients with sepsis to identify differentially expressed genes in the septic state (2, 3). We found changes in CD160 expression as among the most significant quantitative differences in sepsis whole blood gene expression. Analysis of a separate dataset (4) demonstrated significant repression of a long non-coding RNA produced at the CD160 locus in the blood of patients with sepsis. In the datasets we analyzed, changes in coding and non-coding gene expression at the CD160 locus were among the most significant changes in gene expression in the blood of patients with sepsis.

Isolation of differentially expressed genes in wheat caryopses with contrasting starch granule size

2013 ◽  
Vol 8 (3) ◽  
pp. 297-305
Author(s):  
Rita Armonienė ◽  
Kristina Jonavičienė ◽  
Vytautas Ruzgas ◽  
Gintaras Brazauskas
Keyword(s):  
Gene Expression ◽  
Winter Wheat ◽  
Differentially Expressed Genes ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Starch Granule ◽  
Wheat Breeding ◽  
Granule Size ◽  
Differentially Expressed ◽  
Breeding Lines

AbstractIn order to identify genes responsible for starch granule initiation during early development of wheat caryopsis, nine winter wheat breeding lines were studied. Two breeding lines, which are the most diverse in A-type granule size (26.85 µm versus 23.65 µm) were chosen for further differential gene expression analysis in developing caryopses at 10 and 15 days post-anthesis (DPA). cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis resulted in 384 transcript-derived fragments, out of which 18 were identified as being differentially expressed. Six differentially expressed genes, together with the six well-known starch biosynthesis genes, were chosen for semi-quantitative gene expression analysis in developing wheat caryopses at 10 and 15 DPA. This study provides genomic information on 18 genes differentially expressed at early stages of wheat caryopses development and reports on the identification of genes putatively involved in the production of large A-type granules. These genes are targets for further validation on their role in starch granule synthesis control and provide the basis for the development of DNA marker tools in winter wheat breeding for enhanced starch quality.

Gene-Expression Profiling of Graft-Versus-Host Disease by Oligonucleotide Microarrays.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4645-4645
Author(s):  
Jan Verner ◽  
Jitka Kabathova ◽  
Boris Tichy ◽  
Zbynek Zdrahal ◽  
Alexandra Tomancova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Czech Republic ◽  
Differentially Expressed Genes ◽  
Expression Analysis ◽  
Graft Versus Host Disease ◽  
Gene Expression Analysis ◽  
Differentially Expressed ◽  
Oligonucleotide Microarrays ◽  
Post Transplantation ◽  
Graft Versus Host

Abstract Abstract 4645 Background Graft-versus-host disease (GvHD) is the life-threatening complication of allogeneic hematopoietic stem cells transplantation (allo-HSCT). GvHD is mediated by an immune reaction of donor T lymphocytes against recipient's tissues/cells. Acute GvHD (aGvHD) appearing within the first 100 days post transplantation is the most frequent cause of recipient's death and characterization of biomarkers for early prediction of aGvHD or resistance to corticoid treatment could be of great clinical relevance. Biomarker panels for aGvHD are currently extensively studied by proteomic and gene expression based approaches but so far very few markers were described and validated (Kaiser et al., 2004; Baron et al., 2007; Weissinger et al., 2007; Paczesny et al., 2009). Aim In this study, we performed microarray gene expression analysis (whole genome Human OneArray, Phalanx) of 43 leukemia patients who received allo-HSCT. Mononuclear cells isolated from peripheral blood samples (Ficoll-Paque) were collected at i) 14 days before transplantation, ii) 20 and iii) 30 days after transplantation and iv) at the time of aGvHD manifestation. We also performed gene-expression analysis for corticoid-resistant vs. corticoid-sensitive aGvHD cases. Results The SAM supervised analysis of samples collected at day +20 post transplantation revealed set of differentially expressed genes between groups of patients that developed aGvHD vs. aGvHD-free recipients. Among others, genes CASP1 (encoding caspase 1, protein implicated in apoptosis), HLA-DRA (member of MHC class II family) and LILRA3 (leukocyte immunoglobulin-like receptor, subfamily A member 3) showed the highest difference in expression. Gene expression with regard to corticoid response was analyzed at the time of first aGvHD manifestation. The SAM supervised analysis of gene expression between patients with corticoid-sensitive aGvHD (n=10) or aGvHD resistant to corticoid treatment (n=4) revealed a set of significantly differentially expressed genes including NR4A2 (nuclear receptor subfamily 4; member of the steroid-thyroid hormone-retinoid receptor superfamily), DEDD2 (death effector domain containing 2), TREM1 (triggering receptor expressed on myeloid cells 1), TPK1 (thiamin pyrophosphokinase 1) and HBEGF (heparin-binding EGF-like growth factor). Conclusion Oligonucleotide microarrays proved to be a useful tool for expression studies of hematological malignancies and our work shows that they may help to identify markers for early diagnosis/treatment of aGvHD. The limited patients' cohort and their heterogeneity complicate such studies. Our future effort will be focused on experimental group extension, cohort uniformity and verification of the obtained data. This work is supported by the grant NS9683-4/2008 provided by the IGA MH of the Czech Republic, and MSM0021622430 provided by MEYS of Czech Republic Disclosures: No relevant conflicts of interest to declare.

scholarly journals Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yifang Liao ◽  
Ping Li ◽  
Yanxia Wang ◽  
Hong Chen ◽  
Shangwei Ning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Repositioning ◽  
New Drugs ◽  
Differentially Expressed ◽  
Interaction Data ◽  
Competing Endogenous Rna ◽  
Non Coding Rna ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Abstract Background Asthma is a heterogeneous disease characterized by chronic airway inflammation. Long non-coding RNA can act as competing endogenous RNA to mRNA, and play significant role in many diseases. However, there is little known about the profiles of long non-coding RNA and the long non-coding RNA related competing endogenous RNA network in asthma. In current study, we aimed to explore the long non-coding RNA-microRNA-mRNA competing endogenous RNA network in asthma and their potential implications for therapy and prognosis. Methods Asthma-related gene expression profiles were downloaded from the Gene Expression Omnibus database, re-annotated with these genes and identified for asthma-associated differentially expressed mRNAs and long non-coding RNAs. The long non-coding RNA-miRNA interaction data and mRNA-miRNA interaction data were downloaded using the starBase database to construct a long non-coding RNA-miRNA-mRNA global competing endogenous RNA network and extract asthma-related differentially expressed competing endogenous RNA network. Finally, functional enrichment analysis and drug repositioning of asthma-associated differentially expressed competing endogenous RNA networks were performed to further identify key long non-coding RNAs and potential therapeutics associated with asthma. Results This study constructed an asthma-associated competing endogenous RNA network, determined 5 key long non-coding RNAs (MALAT1, MIR17HG, CASC2, MAGI2-AS3, DAPK1-IT1) and identified 8 potential new drugs (Tamoxifen, Ruxolitinib, Tretinoin, Quercetin, Dasatinib, Levocarnitine, Niflumic Acid, Glyburide). Conclusions The results suggested that long non-coding RNA played an important role in asthma, and these novel long non-coding RNAs could be potential therapeutic target and prognostic biomarkers. At the same time, potential new drugs for asthma treatment have been discovered through drug repositioning techniques, providing a new direction for the treatment of asthma.

scholarly journals Genome-wide analysis of blood gene expression in migraine implicates immune-inflammatory pathways

Cephalalgia ◽  
2017 ◽  
Vol 38 (2) ◽  
pp. 292-303 ◽  
Author(s):  
Zachary F Gerring ◽  
Joseph E Powell ◽  
Grant W Montgomery ◽  
Dale R Nyholt
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Whole Blood ◽  
Differentially Expressed ◽  
Expression Data ◽  
Biological Mechanisms ◽  
Blood Gene Expression ◽  
Expression Levels ◽  
Inflammatory Pathways ◽  
Genome Wide

Background Typical migraine is a frequent, debilitating and painful headache disorder with an estimated heritability of about 50%. Although genome-wide association (GWA) studies have identified over 40 single nucleotide polymorphisms associated with migraine, further research is required to determine their biological role in migraine susceptibility. Therefore, we performed a study of genome-wide gene expression in a large sample of 83 migraine cases and 83 non-migraine controls to determine whether altered expression levels of genes and pathways could provide insights into the biological mechanisms underlying migraine. Methods We assessed whole blood gene expression data for 17994 expression probes measured using IlluminaHT-12 v4.0 BeadChips. Differential expression was assessed using multivariable logistic regression. Gene expression probes with a nominal p value < 0.05 were classified as differentially expressed. We identified modules of co-regulated genes and tested them for enrichment of differentially expressed genes and functional pathways using a false discovery rate <0.05. Results Association analyses between migraine and probe expression levels, adjusted for age and gender, revealed an excess of small p values, but there was no significant single-probe association after correction for multiple testing. Network analysis of pooled expression data identified 10 modules of co-expressed genes. One module harboured a significant number of differentially expressed genes and was strongly enriched with immune-inflammatory pathways, including multiple pathways expressed in microglial cells. Conclusions These data suggest immune-inflammatory pathways play an important role in the pathogenesis, manifestation, and/or progression of migraine in some patients. Furthermore, gene-expression associations are measurable in whole blood, suggesting the analysis of blood gene expression can inform our understanding of the biological mechanisms underlying migraine, identify biomarkers, and facilitate the discovery of novel pathways and thus determine new targets for drug therapy.

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