USING RNA-SEQ DATASETS FROM GEO DATABASE IDENTIFICATION OF POTENTIAL GENETIC BIOMARKERS FOR DILATED CARDIOMYOPATHY

In this study, we investigated the role of DNA methylation [5-methylcytosine (5mC)] and 5-hydroxymethylcytosine (5hmC), epigenetic modifications that regulate gene activity, in dilated cardiomyopathy (DCM). A MYBPC3 mutant mouse model of DCM was compared with wild type and used to profile genomic 5mC and 5hmC changes by Chip-seq, and gene expression levels were analyzed by RNA-seq. Both 5mC-altered genes (957) and 5hmC-altered genes (2,022) were identified in DCM hearts. Diverse gene ontology and KEGG pathways were enriched for DCM phenotypes, such as inflammation, tissue fibrosis, cell death, cardiac remodeling, cardiomyocyte growth, and differentiation, as well as sarcomere structure. Hierarchical clustering of mapped genes affected by 5mC and 5hmC clearly differentiated DCM from wild-type phenotype. Based on these data, we propose that genomewide 5mC and 5hmC contents may play a major role in DCM pathogenesis. NEW & NOTEWORTHY Our data demonstrate that development of dilated cardiomyopathy in mice is associated with significant epigenetic changes, specifically in intronic regions, which, when combined with gene expression profiling data, highlight key signaling pathways involved in pathological cardiac remodeling and heart contractile dysfunction.

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Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq

International Journal of Genomics ◽

10.1155/2018/7647980 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Zehra Omeroğlu Ulu ◽

Salih Ulu ◽

Soner Dogan ◽

Bilge Guvenc Tuna ◽

Nehir Ozdemir Ozgenturk

Keyword(s):

Calorie Restriction ◽

Critical Role ◽

Gene Expression Omnibus ◽

Cdna Libraries ◽

Rna Seq ◽

Illumina Hiseq ◽

Ncbi Gene Expression Omnibus ◽

Important Player ◽

Feeding Regimes ◽

Geo Database

Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p<0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus.

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Abstract 232: Studies of Cardiac transcriptome and Dilated Cardiomyopathy-causative genes in zebrafish

Circulation Research ◽

10.1161/res.115.suppl_1.232 ◽

2014 ◽

Vol 115 (suppl_1) ◽

Author(s):

Yu-Huan Shih ◽

Yuji Zhang ◽

Tim Olson ◽

Xiaolei Xu

Keyword(s):

Dilated Cardiomyopathy ◽

System Biology ◽

Underlying Mechanism ◽

The Novel ◽

Rna Seq ◽

Adult Zebrafish ◽

Future System ◽

Novel Variants ◽

Vertebrate Model ◽

Definition Of

Background: Rapid advance of genome technologies accelerate the discovery of genetic basis of cardiomyopathy and heart failure and also enable system biology studies to pinpoint underlying mechanism. However, the limited throughput of mammalian models restricted the number of genes that can be studied in a particular lab. Adult zebrafish has been recently pursued as a new model with higher throughput. However, as a non-mammalian model, its conservation is not tested. Objective: To assess the conservation of zebrafish for genetic studies of human dilated cardiomyopathy (DCM) via transcriptome analysis of 51 known DCM-causative genes. Methods and Results: By conducting RNA-sequencing (RNA-seq) analysis of larva and adult zebrafish, we identified genes with high expression level in the heart and fetal gene program using differential expression between embryonic and adult stages. We then searched zebrafish orthologues for 51 reported human DCM-causative or associated genes and identified zebrafish orthologues for 49 of them. While 30 genes have a single orthologue, 14 genes have two homologues and the remaining 5 genes have more than three. We then applied the transcriptome data to prioritize these homologues for the 19 DCM causative genes with more than one homologue. Based on the cardiac abundance and cardiac enrichment hypothesis, we are able to recommend a single zebrafish homologue of high priority for 12 out of 19 DCM genes, 2 zebrafish homologues of high priority for ACTC1. Interestingly, our expressional data suggested zebrafish othologues for human MYH6 and MYH7 , respectively. Similar to that in mammals, these two zebrafish othologues are oppositely expressed during zebrafish embryonic and adult stage. Conclusions: Orthologues for the majority of DCM causative genes can be found in Zebrafish, supporting its usage as a conserved vertebrate model for studying DCM. The definition of cardiac transcriptome in zebrafish will facilitate the future system biology studies. This vertebrate model with higher throughput can be further leveraged to validate the novel variants identified from human patients, to understand underlying signaling pathways and to develop novel therapeutics.

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Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy

American Journal of Veterinary Research ◽

10.2460/ajvr.77.7.693 ◽

2016 ◽

Vol 77 (7) ◽

pp. 693-699 ◽

Cited By ~ 1

Author(s):

Steven G. Friedenberg ◽

Lhoucine Chdid ◽

Bruce Keene ◽

Barbara Sherry ◽

Alison Motsinger-Reif ◽

...

Keyword(s):

Dilated Cardiomyopathy ◽

Differentially Expressed ◽

Rna Seq

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Integrated analysis reveals the alterations that LMNA interacts with euchromatin in LMNA mutation-associated dilated cardiomyopathy

Clinical Epigenetics ◽

10.1186/s13148-020-00996-1 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Xiaolin Zhang ◽

Xiuli Shao ◽

Ruijia Zhang ◽

Rongli Zhu ◽

Rui Feng

Keyword(s):

Dilated Cardiomyopathy ◽

Molecular Pathogenesis ◽

Integrated Analysis ◽

Rna Seq ◽

Lmna Mutation ◽

Differential Binding ◽

Key Genes ◽

Downstream Analysis ◽

Pathological Disease

Abstract Background Dilated cardiomyopathy (DCM) is a serious cardiac heterogeneous pathological disease, which may be caused by mutations in the LMNA gene. Lamins interact with not only lamina-associated domains (LADs) but also euchromatin by alone or associates with the lamina-associated polypeptide 2 alpha (LAP2α). Numerous studies have documented that LMNA regulates gene expression by interacting with LADs in heterochromatin. However, the role of LMNA in regulating euchromatin in DCM is poorly understood. Here, we determine the differential binding genes on euchromatin in DCM induced by LMNA mutation by performing an integrated analysis of bioinformatics and explore the possible molecular pathogenesis mechanism. Results Six hundred twenty-three and 4484 differential binding genes were identified by ChIP-seq technology. The ChIP-seq analysis results and matched RNA-Seq transcriptome data were integrated to further validate the differential binding genes of ChIP-seq. Five and 60 candidate genes involved in a series of downstream analysis were identified. Finally, 4 key genes (CREBBP, PPP2R2B, BMP4, and BMP7) were harvested, and these genes may regulate LMNA mutation-induced DCM through WNT/β-catenin or TGFβ-BMP pathways. Conclusions We identified four key genes that may serve as potential biomarkers and novel therapeutic targets. Our study also illuminates the possible molecular pathogenesis mechanism that the abnormal binding between LMNA or LAP2α-lamin A/C complexes and euchromatin DNA in LMNA mutations, which may cause DCM through the changes of CREBBP, PPP2R2B, BMP4, BMP7 expressions, and the dysregulation of WNT/β-catenin or TGFβ-BMP pathways, providing valuable insights to improve the occurrence and development of DCM. Graphic abstract

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m6A Regulator-Mediated Methylation Modification Patterns and Characteristics of Immunity in Blood Leukocytes of COVID-19 Patients

Frontiers in Immunology ◽

10.3389/fimmu.2021.774776 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiangmin Qiu ◽

Xiaoliang Hua ◽

Qianyin Li ◽

Qin Zhou ◽

Juan Chen

Keyword(s):

T Cells ◽

Virus Infection ◽

T Cell Activation ◽

Cell Activation ◽

Apache Ii Score ◽

Rna Seq ◽

Blood Leukocytes ◽

Cluster A ◽

Score Apache ◽

Geo Database

Both RNA N6-methyladenosine (m6A) modification of SARS-CoV-2 and immune characteristics of the human body have been reported to play an important role in COVID-19, but how the m6A methylation modification of leukocytes responds to the virus infection remains unknown. Based on the RNA-seq of 126 samples from the GEO database, we disclosed that there is a remarkably higher m6A modification level of blood leukocytes in patients with COVID-19 compared to patients without COVID-19, and this difference was related to CD4+ T cells. Two clusters were identified by unsupervised clustering, m6A cluster A characterized by T cell activation had a higher prognosis than m6A cluster B. Elevated metabolism level, blockage of the immune checkpoint, and lower level of m6A score were observed in m6A cluster B. A protective model was constructed based on nine selected genes and it exhibited an excellent predictive value in COVID-19. Further analysis revealed that the protective score was positively correlated to HFD45 and ventilator-free days, while negatively correlated to SOFA score, APACHE-II score, and crp. Our works systematically depicted a complicated correlation between m6A methylation modification and host lymphocytes in patients infected with SARS-CoV-2 and provided a well-performing model to predict the patients’ outcomes.

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Identification of Functional lncRNAs Associated With Ovarian Endometriosis Based on a ceRNA Network

Frontiers in Genetics ◽

10.3389/fgene.2021.534054 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jian Bai ◽

Bo Wang ◽

Tian Wang ◽

Wu Ren

Keyword(s):

Gene Expression Omnibus ◽

Reproductive Age ◽

Differentially Expressed ◽

Rna Seq ◽

Ovarian Endometriosis ◽

Diagnostic Biomarkers ◽

Cerna Network ◽

Competing Endogenous Rnas ◽

Gynecological Disease ◽

Geo Database

BackgroundEndometriosis is a common gynecological disease affecting women of reproductive age; however, the mechanisms underlying this condition are not fully clear. The aim of this study was to identify functional long non-coding RNAs (lncRNAs) associated with ovarian endometriosis for potential use as biomarkers and therapeutic targets.MethodsRNA-seq profiles of paired ectopic (EC) and eutopic (EU) endometrial samples from patients with ovarian endometriosis were downloaded from the publicly available Gene Expression Omnibus (GEO) database. Bioinformatics algorithms were used to construct a network of ovarian endometriosis-related competing endogenous RNAs (ceRNAs) and to detect functional lncRNAs.ResultsA total of 4,213 mRNAs, 1,474 lncRNAs, and 221 miRNAs were identified as being differentially expressed between EC and EU samples, and an ovarian endometriosis-related ceRNA network was constructed through analysis of these differentially expressed RNAs. H19 and GS1-358P8.4 were identified as key ovarian endometriosis-related lncRNAs through topological feature analysis, and RP11-96D1.10 was identified using a random walk with restart algorithm.ConclusionBased on bioinformatics analysis of a ceRNA network, we identified the lncRNAs H19, GS1-358P8.4, and RP11-96D1.10 as being strongly associated with ovarian endometriosis. These three lncRNAs hold potential as targets for medical therapy and as diagnostic biomarkers. Further studies are needed to elucidate the detailed biological function of these lncRNAs in the pathogenesis of endometriosis.

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Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy

BioMed Research International ◽

10.1155/2021/6653802 ◽

2021 ◽

Vol 2021 ◽

pp. 1-29

Author(s):

Li Liu ◽

Jianjun Huang ◽

Yan Liu ◽

Xingshou Pan ◽

Zhile Li ◽

...

Keyword(s):

Dilated Cardiomyopathy ◽

Differentially Expressed ◽

Molecular Characteristics ◽

Rna Seq ◽

Frequent Mutation ◽

Protein Protein Interaction ◽

Molecular Features ◽

Differentially Methylated Genes ◽

And Control ◽

Control Samples

Objective. Multiple genes have been identified to cause dilated cardiomyopathy (DCM). Nevertheless, there is still a lack of comprehensive elucidation of the molecular characteristics for DCM. Herein, we aimed to uncover putative molecular features for DCM by multiomics analysis. Methods. Differentially expressed genes (DEGs) were obtained from different RNA sequencing (RNA-seq) datasets of left ventricle samples from healthy donors and DCM patients. Furthermore, protein-protein interaction (PPI) analysis was then presented. Differentially methylated genes (DMGs) were identified between DCM and control samples. Following integration of DEGs and DMGs, differentially expressed and methylated genes were acquired and their biological functions were analyzed by the clusterProfiler package. Whole exome sequencing of blood samples from 69 DCM patients was constructed in our cohort, which was analyzed the maftools package. The expression of key mutated genes was verified by three independent datasets. Results. 1407 common DEGs were identified for DCM after integration of the two RNA-seq datasets. A PPI network was constructed, composed of 171 up- and 136 downregulated genes. Four hub genes were identified for DCM, including C3 ( degree = 24 ), GNB3 ( degree = 23 ), QSOX1 ( degree = 21 ), and APOB ( degree = 17 ). Moreover, 285 hyper- and 321 hypomethylated genes were screened for DCM. After integration, 20 differentially expressed and methylated genes were identified, which were associated with cell differentiation and protein digestion and absorption. Among single-nucleotide variant (SNV), C>T was the most frequent mutation classification for DCM. MUC4 was the most frequent mutation gene which occupied 71% across 69 samples, followed by PHLDA1, AHNAK2, and MAML3. These mutated genes were confirmed to be differentially expressed between DCM and control samples. Conclusion. Our findings comprehensively analyzed molecular characteristics from the transcriptome, epigenome, and genome perspectives for DCM, which could provide practical implications for DCM.

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Abstract 14930: Involvement of Chloride Channel (clic) in Myocardial Fibrosis of Pressure-overload Model Mice and Dilated Cardiomyopathy Patients

Circulation ◽

10.1161/circ.142.suppl_3.14930 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Gaku Oguri ◽

Toshiaki Nakajima ◽

Nomura Seitaro ◽

Nakajima Takahumi ◽

Hironobu Kikuchi ◽

...

Keyword(s):

Heart Failure ◽

Growth Factor ◽

Cardiac Hypertrophy ◽

Dilated Cardiomyopathy ◽

Single Cell ◽

Chloride Channel ◽

Ventricular Myocytes ◽

Pressure Overload ◽

Rna Seq ◽

Single Ventricular Myocytes

Introduction: Pressure overload induces cardiac hypertrophy, electrical remodeling due to changes in various channels, and eventually leads to fibrosis, hardening of the heart, left ventricular diastolic dysfunction, and heart failure. Chloride channels (chloride intracellular channels, Clic) are localized in both plasma membranes and intracellular organelles of various cells, and have recently been reported to be associated with atrial fibrosis. In this study, we examined single-cell RNA-seq analysis of cardiomyocytes for changes in Clic using a pressure overload model due to transverse aortic coarctation (TAC). In addition, a similar analysis was performed on ventricular myocytes in dilated cardiomyopathy. Methods: Single ventricular myocytes were collected from the free wall of the left ventricle after TAC by collagenase treatment in the cardiac hypertrophy phase (3 days after TAC, 1 or 2 weeks (W)) and the heart failure phase (4,8W). The expression of various genes in ventricular myocytes was analyzed for single cells by RNA-seq and compared with sham mice. In addition, a similar study was performed from single ventricular myocytes obtained from dilated cardiomyopathy patients and donors. Results: The expression of myosin heavy chain β (Myh7), a fetal gene, was increased by pressure overload, but the expression of BNP and ANP genes was increased along with the expression of adult Myh6. Regarding Clic, Clic1,4 and 5 increased as compared with Sham mice. Clic1, Clic1 and 4 increased from 3d, and at 8W, Clic1, 4, and 5 also increased . The expression level of these Clic genes is associated with the genes associated with fibrosis (Col4a1, 4a2, 6a2, connective tissue growth factor (CTGF), transforming growth factor-beta 2 (TGFβ2). The KEGG pathway analysis using DAVID for genes with significant associations with Clic1,4, and 5 revealed a strong association with activation of Focal adhesion pathway. Single cell RNA-seq analysis of single ventricular myocytes from patients with dilated cardiomyopathy also showed a increase in CLIC4 and 5 genes compared to healthy donors. Conclusions: Single cell RNA of ventricular myocytes -seq analysis revealed the involvement of chloride channel Clic in myocardial fibrosis and structural remodeling in failing hearts.

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Meta-Analysis of Dilated Cardiomyopathy Using Cardiac RNA-Seq Transcriptomic Datasets

Genes ◽

10.3390/genes11010060 ◽

2020 ◽

Vol 11 (1) ◽

pp. 60 ◽

Cited By ~ 6

Author(s):

Ahmad Alimadadi ◽

Patricia B. Munroe ◽

Bina Joe ◽

Xi Cheng

Keyword(s):

Dilated Cardiomyopathy ◽

Meta Analysis ◽

Rna Seq ◽

Upstream Regulator ◽

Core Set ◽

Common Causes ◽

Significant Pathway ◽

Human Left Ventricle ◽

Upregulated Genes ◽

Cardiovascular Functions

Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Several studies have used RNA-sequencing (RNA-seq) to profile differentially expressed genes (DEGs) associated with DCM. In this study, we aimed to profile gene expression signatures and identify novel genes associated with DCM through a quantitative meta-analysis of three publicly available RNA-seq studies using human left ventricle tissues from 41 DCM cases and 21 control samples. Our meta-analysis identified 789 DEGs including 581 downregulated and 208 upregulated genes. Several DCM-related genes previously reported, including MYH6, CKM, NKX2–5 and ATP2A2, were among the top 50 DEGs. Our meta-analysis also identified 39 new DEGs that were not detected using those individual RNA-seq datasets. Some of those genes, including PTH1R, ADAM15 and S100A4, confirmed previous reports of associations with cardiovascular functions. Using DEGs from this meta-analysis, the Ingenuity Pathway Analysis (IPA) identified five activated toxicity pathways, including failure of heart as the most significant pathway. Among the upstream regulators, SMARCA4 was downregulated and prioritized by IPA as the top affected upstream regulator for several DCM-related genes. To our knowledge, this study is the first to perform a transcriptomic meta-analysis for clinical DCM using RNA-seq datasets. Overall, our meta-analysis successfully identified a core set of genes associated with DCM.

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