Transcriptome and translatome of cardiomyocytes exposed to hypoxia in vivo and in vitro
Ontology highlight
ABSTRACT:
INSTRUMENT(S): HiSeq X Ten
ORGANISM(S): Rattus norvegicus
SUBMITTER: Zhihui Zhang
PROVIDER: E-MTAB-9541 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Hypoxia as a crucial pathogenesis factor usually results in huge harmful effects on cardiac injury and dysfunction. In our previous study (PMID: 33294289), We observe a series of differential expressed genes between transcription and translation, which may be attributed to the hypoxia-specific binding affinity of Nuclear cap-binding subunit 3 (NCBP3) at 5’ un-translation region of target genes. But the underlying molecular mechanism of NCBP3 for gene translation modulation remains unclear. Here, we conducted RIP-seq of N6-Methyladenosine methylation in H9C2 cells with the conditions of normoxic, hypoxic and with additional NCBP3 knockdown.
2021-06-30 | E-MTAB-10682 | biostudies-arrayexpress
Project description:Gene expression analysis of 7d-old Arabidopsis seedlings exposed to short term (2 h) hypoxia, long term (9 h) hypoxia, and 1 h reoxygenation after long term (9 h) hypoxia to evaluate the regulation of gene expression at the level of translation. Experiment Overall Design: 30 samples, 5 conditions (2 hr hypoxia stress, 2hr non-stress, 9 hr hypoxia stress , 9 hr non-stress, 9 hr hypoxia with 1 hr recovery), 2 RNA pools (Total mRNA and polysomal mRNA), 3 replicates
2008-10-20 | E-GEOD-9719 | biostudies-arrayexpress
Project description:Acute occlusion of a coronary artery results in swift tissue necrosis. Bordering areas of the infarcted myocardium may also experience impaired blood supply and reduced oxygen delivery leading to altered metabolic and mechanical processes. While transcriptional changes in hypoxic cardiomyocytes are well-studied, little is known about the proteins that are actively secreted from these cells. We established a novel secretome analysis of cardiomyocytes by combining stable isotope labeling and click chemistry with subsequent mass spectrometry analysis. Further functional validation experiments included ELISA measurement of human samples, murine LAD ligation and adeno-associated virus (AAV) 9-mediated in vivo overexpression in mice. The presented approach is feasible for the analysis of the secretome of primary cardiomyocytes without serum starvation. 1026 proteins were identified to be secreted within 24 hours, indicating a 5-fold increase in detection compared to former approaches. Among them, a variety of proteins have so far not been explored in the context of cardiovascular pathologies. One of the most strongly upregulated secreted factors upon hypoxia was proprotein convertase subtilisin/kexin type 6 (PCSK6). Validation experiments revealed an increase of PCSK6 on mRNA and protein level in hypoxic cardiomyocytes. PCSK6 expression was elevated in hearts of mice following 3 days of ligation of the left anterior descending artery, a finding confirmed by immunohistochemistry. ELISA measurements in human serum also indicate distinct kinetics for PCSK6 in patients suffering from acute myocardial infarction, with a peak on day 3 post-infarction. Transfer of PCSK6-depleted cardiomyocyte secretome resulted in decreased expression of collagen I and III in fibroblasts compared to control treated cells, and siRNA mediated knockdown of PCSK6 in cardiomyocytes impacted transforming growth factor-β activation and mothers against decapentaplegic homolog 3 (SMAD3) translocation in fibroblasts. An Adeno-associated virus (AAV) 9-mediated, cardiomyocyte-specific overexpression of PCSK6 in mice resulted in increased collagen expression and cardiac fibrosis as well as decreased left ventricular function after myocardial infarction. In conclusion, a novel mass spectrometry-based approach allows the investigation of the secretome of primary cardiomyocytes. Analysis of hypoxia-induced secretion led to the identification of PCSK6 to be crucially involved in cardiac remodeling after acute myocardial infarction. Secretome analysis was performed on neonatal rat ventricular cardiomyocytes (NRVCMs) which were incubated under hypoxic conditions (1.5% O2, 5% CO2, 93.5% N2) for 12 (Hypoxia 0-12h), 24 (Hypoxia 0-24h) and 30 (Hypoxia 24-30h) hours. Furthermore, knockdown (KD) of PCSK6 in vitro mediated by small interfering RNA (siRNA) was performed to investigate changes in the secretome of cardiomyocytes with PCSK6 KD vs. control (control siRNA) during 24 hours of hypoxia (PCSK6 KD 0-24h). Cells were pulse-labeled with AHA (L-azidohomoalanine) and SILAC (stable isotope labeling with amino acids in cell culture) for 12 (Hypoxia 0-12h), 24 (Hypoxia 0-24h/PCSK6 KD 0-24h) and 6 hours (Hypoxia 24-30h). For Hypoxia 0-12h 3 replicates, Hypoxia 0-24h 6 replicates, PCSK6 KD 0-24h 3 Replicates and Hypoxia 24-30h 2 replicates were performed with label-swap.
2020-03-05 | PXD016178 | Pride
Project description:Purpose: The physiological cardiac hypertrophy is an adaptive condition that does not associate with myocyte cell death while pathological hypertrophy is a maladaptive condition associated with myocyte cell death. Alpha-2 macroglobulin (α-2M) an acute phase protein induces cardiac hypertrophy via the ERK1,2 and PI3K/Akt signaling. This study is aimed at exploring the miRNome of α-2M induced hypertrophied cardiomyocytes and to understand the role of miRNAs in determination of pathological and physiological hypertrophy. Methods: Hypertrophy was induced in H9c2 cardiomyoblasts using alpha-2 macroglobulin. The induction of hypertrophy is confirmed by microscopy and gene expression studies. Subsequently, the total RNA was isolated and small RNA sequencing was executed in Illumina HiSeq 2000. Results: Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during hypertrophy. Among the differentially expressed candidates, miR-99 family (miR-99a, miR-99b and miR-100) showed significant downregulation upon α-2M treatment while isoproterenol treatment (pathological hypertrophy) upregulated their expression. The binding site for Egr1 transcription factor was identified in the promoter region of miR-99 family, and interestingly all miRNAs with Egr1 binding site proven by ChIP-Seq were downregulated during physiological hypertrophy Conclusions: The results proved Egr-1 mediated regulation of miR-99 family determines the uniqueness of pathological and physiological hypertrophy. Upregulated miR-99 expression during pathological hypertrophy suggests that it can be a valuable diagnostic marker and potential therapeutic target for cardiac hypertrophy and heart failure. Small RNA profiles of control and hypertrophied cardiomyocyte H9c2 cells were generated by deep sequencing using Illumina HiSeq 2000
2015-11-01 | E-GEOD-73597 | biostudies-arrayexpress
Project description:The rat cardio-myoblast cell line H9C2 has emerged as an important tool for studying cardiac development and toxicology. We present here a rigorous proteomic analysis that for the first time studied changes of proteins during H9C2 differentiation into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed early changes in protein pathways that enable cardiac muscle morphogenesis/contraction and suggested an involvement of proteins relevant to sphingolipid synthesis. This early differentiation was followed by differentiation-induced alterations in cation transport and beta-oxidation at later time points. Applying a two-way ANOVA to study the temporal profile of H9C2 differentiation in further detail revealed eight clusters of co-regulated proteins that could be associated to early, late, continuous and transient up- and downregulation. Subsequent Reactome pathway analysis based on these eight clusters further corroborated and detailed the results of the GO analysis. Specifically, this analysis confirmed proteins related to pathways in muscle contraction as early and transiently upregulated, and proteins relevant to ECM matrix organization as early downregulated, while changes related to cardiac metabolism occurred at later time points. Our results are in line with a ‘function follows form’ model of differentiation, whereby early and transient changes of cellular morphology enable subsequent changes that are relevant for the characteristic physiology of cardiac cells.
2018-11-07 | PXD006115 | Pride
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2021-10-06 | E-MTAB-10720 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10912 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10913 | biostudies-arrayexpress
Project description:In this study, we performed temporal profiling of transcriptome and chromatin accessibility in HL-1 cells for understanding the molecular mechanisms underlying cardiac responses to hypoxia. We collected HL-1 cells under four conditions (4 h and 8 h of hypoxia exposure, 24 h reoxygenation and the normal condition), applied RNA-seq and ATAC-seq to them and performed pairwise comparison of gene expression and open chromatin status on a genome-wide scale.
2021-12-31 | E-MTAB-8814 | biostudies-arrayexpress
Project description:Background: Hypoxia can affect aerobic organisms profoundly. Biological responses to extreme hypoxia have been well studied. However, it is not well characterized how living organisms respond to mild hypoxia, and how they distinguish different levels of hypoxia. Results: We examined the transcriptional responses of locusts using microarrays to reveal their strategies to cope with mild hypoxia. Mitochondrial activities were systemically suppressed, mainly involving energy production and mitochondrial biogenesis. The functions of endoplasmic reticulum were activated to clear the dysfunctional proteins and rescue newly synthesized proteins. Glucose in cytosol was shunted from glycolysis to pentose phosphate pathway probably to tackle the oxidative stress by enhancing the production of reductive forces. Conclusions: LocustsM-bM-^@M-^Y responses to mild hypoxia differ from that to severe hypoxia . In severe hypoxia, glucose resources are shunted to glycolysis to produce ATP and tackle energy crisis; however, in mild hypoxia, they are diverted to produce reductive forces and deal with oxidative stress. Locusts are capable of distinguishing different levels of hypoxia and initiating proper defenses. Simulated 4km altitude hypoxia treatment vs. normoxia control;direct comparison on 6 separate microarrays; each microarray compares one biological replicate of treatment and control; each biological replicate contains 10 individuals
2012-12-12 | E-GEOD-33898 | biostudies-arrayexpress