scholarly journals Characterization of circular RNA transcriptomes in psoriasis and atopic dermatitis reveals disease‐specific expression profiles

2020 ◽  
Author(s):  
Liviu I. Moldovan ◽  
Lam C. Tsoi ◽  
Uppala Ranjitha ◽  
Henrik Hager ◽  
Stephen Weidinger ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Expression Profiles ◽  
Circular Rna ◽  
Specific Expression ◽  
Disease Specific

scholarly journals Characterization of Circular RNA Transcriptomes in Psoriasis and Atopic Dermatitis Reveals Disease-specific Expression Profiles

2020 ◽  
Author(s):  
Liviu Ionut Moldovan ◽  
Lam Alex Tsoi ◽  
Stephen Weidinger ◽  
Johann Gudjonsson ◽  
Jørgen Kjems ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Skin Diseases ◽  
Expression Profiles ◽  
Circular Rna ◽  
Detection Algorithm ◽  
Healthy Skin ◽  
Inflammatory Skin Diseases ◽  
Specific Expression ◽  
Lesional Skin ◽  
Inflammatory Skin

AbstractBackgroundAtopic dermatitis (AD) and psoriasis, two chronic inflammatory skin diseases, affect a large number of individuals worldwide, and are associated with various comorbidities. Circular RNA (circRNA) constitute a major class of non-coding RNAs that have been implicated in many human diseases, although their potential involvement in inflammatory skin diseases remains elusive.ObjectivesTo compare and contrast the circRNA expression landscapes in paired lesional and non-lesional skin from psoriasis and AD patients relative to skin from unaffected individuals. Moreover, to correlate circRNA expression to disease severity.MethodsWe analyzed high-depth RNA-seq data from paired lesional and non-lesional skin samples from 27 AD patients, 28 psoriasis patients, and 38 healthy controls. CircRNAs and their cognate linear transcripts were quantified using the circRNA detection algorithm, CIRI2.ResultsWe identified 39,286 unique circRNAs in total and found that psoriasis and AD lesional skin could be distinguished from non-lesional and healthy skin based on circRNA expression landscapes. In general, circRNAs were less abundant in lesional relative to non-lesional and healthy skin. Differential expression analyses revealed many significantly downregulated circRNAs, mainly in psoriasis lesional skin, and a strong correlation between psoriasis and AD-related circRNA expression changes was observed. A subset of circRNAs, including ciRS-7, was specifically dysregulated in psoriasis and show promise as biomarkers for discriminating AD from psoriasis.ConclusionPsoriasis and circRNA transcriptomes share expression features, including a global downregulation, but only psoriasis is characterized by several circRNAs being dysregulated independently of their cognate linear transcripts.

scholarly journals Circular RNA Expression Profiles and Features in NAFLD Mice: A Study Using RNA-Seq Data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously.Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development.Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

Characterization of IgE–Reactive Autoantigens in Atopic Dermatitis 1. Subcellular Distribution and Tissue–Specific Expression

1999 ◽  
Vol 120 (2) ◽  
pp. 108-116 ◽  
Author(s):  
Susanne Seiberler ◽  
Agnes Bugajska-Schretter ◽  
Peter Hufnagl ◽  
Bernd R. Binder ◽  
Johannes Stöckl ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Subcellular Distribution ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously. Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development. Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Genome ◽  
2018 ◽  
Vol 61 (5) ◽  
pp. 337-347 ◽  
Author(s):  
Tuanhui Ren ◽  
Zhuanjian Li ◽  
Yu Zhou ◽  
Xuelian Liu ◽  
Ruili Han ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Muscle Development ◽  
Target Genes ◽  
Expression Profiles ◽  
Economic Value ◽  
Muscle Quality ◽  
Specific Expression ◽  
Chicken Muscle ◽  
Molecular Regulatory Mechanisms

Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs.

scholarly journals debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues

2020 ◽  
Vol 36 (12) ◽  
pp. 3927-3929 ◽  
Author(s):  
Lulu Chen ◽  
Chiung-Ting Wu ◽  
Niya Wang ◽  
David M Herrington ◽  
Robert Clarke ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Software Tool ◽  
R Package ◽  
Supplementary Information ◽  
Tissue Cell ◽  
Deconvolution Method ◽  
Imaging Data ◽  
Specific Expression ◽  
Knowledge Incorporation

Abstract Summary We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes based on bulk expression profiles. We implement an R package, deconvolution by Convex Analysis of Mixtures (debCAM) that can automatically detect tissue/cell-specific markers, determine the number of constituent subtypes, calculate subtype proportions in individual samples and estimate tissue/cell-specific expression profiles. We demonstrate the performance and biomedical utility of debCAM on gene expression, methylation, proteomics and imaging data. With enhanced data preprocessing and prior knowledge incorporation, debCAM software tool will allow biologists to perform a more comprehensive and unbiased characterization of tissue remodeling in many biomedical contexts. Availability and implementation http://bioconductor.org/packages/debCAM. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously. Methods A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development. Conclusions Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals Characterization of Lipid and Lipid Droplet Metabolism in Human HCC

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 512 ◽  
Author(s):  
Nikolaus Berndt ◽  
Johannes Eckstein ◽  
Niklas Heucke ◽  
Robert Gajowski ◽  
Martin Stockmann ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Lipid Metabolism ◽  
Expression Profiles ◽  
Primary Liver Cancer ◽  
Fatty Acid Uptake ◽  
Metabolic Phenotype ◽  
Acid Uptake ◽  
Specific Expression ◽  
Very High

Human hepatocellular carcinoma (HCC) is the most common type of primary liver cancer in adults and the most common cause of death in people with cirrhosis. While previous metabolic studies of HCC have mainly focused on the glucose metabolism (Warburg effect), less attention has been paid to tumor-specific features of the lipid metabolism. Here, we applied a computational approach to analyze major pathways of fatty acid utilization in individual HCC. To this end, we used protein intensity profiles of eleven human HCCs to parameterize tumor-specific kinetic models of cellular lipid metabolism including formation, enlargement, and degradation of lipid droplets (LDs). Our analysis reveals significant inter-tumor differences in the lipid metabolism. The majority of HCCs show a reduced uptake of fatty acids and decreased rate of β-oxidation, however, some HCCs display a completely different metabolic phenotype characterized by high rates of β-oxidation. Despite reduced fatty acid uptake in the majority of HCCs, the content of triacylglycerol is significantly enlarged compared to the tumor-adjacent tissue. This is due to tumor-specific expression profiles of regulatory proteins decorating the surface of LDs and controlling their turnover. Our simulations suggest that HCCs characterized by a very high content of triglycerides comprise regulatory peculiarities that render them susceptible to selective drug targeting without affecting healthy tissue.

Changes in protein profiles during course of experimental glomerulonephritis

2009 ◽  
Vol 296 (1) ◽  
pp. F186-F193 ◽  
Author(s):  
Khurram Nazeer ◽  
Michael G. Janech ◽  
Jim J.-C. Lin ◽  
Kevin J. Ryan ◽  
John M. Arthur ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Two Dimensional Gel Electrophoresis ◽  
Glomerular Cell ◽  
Capping Protein ◽  
Experimental Glomerulonephritis ◽  
Disease Specific

Better characterization of the molecular mechanisms underlying glomerular cell proliferation may improve our understanding of the pathogenesis of glomerulonephritis and yield disease-specific markers. We used two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) to generate expression profiles of glomerular proteins in the course of anti-Thy-1 nephritis. Glomeruli were isolated from Wistar rats by sieving, and proteins were separated by 2DE. In preliminary studies using normal rats, we identified known glomerular proteins from microfilaments [tropomyosin (Tm)] and intermediate filaments (vimentin and lamin A), proteins involved in assembly (α-actinin-4, F-actin capping protein) and membrane cytoskeletal linking (ezrin), as well as several enzymes (protein disulfide isomerase, ATP synthase, and aldehyde dehydrogenase). Comparison of glomerular protein abundance between normal rats and rats in the early phase of anti-Thy-1 nephritis yielded 28 differentially expressed protein spots. MS analysis identified 16 differentially expressed proteins including Tm. Altered Tm abundance in the course of anti-Thy-1 nephritis was confirmed, and specific isoforms were characterized by Western blotting. We demonstrated a complex change in Tm isoform abundance in the course of anti-Thy-1 nephritis. The early mesangiolytic phase of the disease was characterized by decreased abundance of low-molecular-weight isoforms Tm5a/5b and increased abundance of high-molecular-weight isoforms Tm6, Tm1, Tm2, and Tm3. The late proliferative phase of the disease was associated with increased abundance of isoforms Tm5a/5b, Tm6, and Tm1 and decreased abundance of Tm3. Isoforms Tm4 and Tm5 remained unchanged in the course of this model of experimental glomerulonephritis. Characterization of Tm isoform abundance in the course of clinical glomerulonephritis may identify disease-specific markers.

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