ATAC-seq Profiling of Adult Mouse Cardiomyocytes Treated with AAV9-cTnT-Rbm22 in MI Model
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE311241 | GEO | 2026/02/12
REPOSITORIES: GEO
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Project description:Purpose: The purpose of this study is to identify chromatin alterations regulated by RBM22. We performed ATAC-sequencing in primary cultured neonatal mouse cardiomyocytes transfected with control siRNA or Rbm22 siRNA. Methods: Cardiomyocytes were isolated from 1-day-old C57BL/6J mice and cultured in DMEM with 10% fetal bovine serum at 37°C in an atmosphere with 5% CO2. Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments. Cardiomyocytes were transfected with control siRNA or Rbm22 siRNA for 48 hours. Results: We identified regions of chromatin that were altered between cardiomyocytes transfected with the indicated siRNAs.
2026-02-12 | GSE295696 | GEO
Project description:Purpose:The purpose of this study is to identify genes that are either activated or silenced in cardiomyocytes treated with siRNA targeting RBM22 (si-Rbm22) compared to control siRNA (si-Control). Gene expression differences between the two samples were identified using transcriptome profiling (RNA-seq) analysis. Methods: Primary neonatal mouse cardiomyocytes were isolated from neonatal C57BL/6J mice at postnatal day 1.Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments. Neonatal cardiomyocytes in primary culture were transfected with either siRNA targeting Rbm22 (si-Rbm22) or a non-targeting control siRNA (si-Control) for 48 h, of which RNA profiles were generated by deep sequencing using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome and identified numerous genes with significant mRNA variation between cardiomyocytes transfected with the indicated siRNAs.
2026-02-12 | GSE295695 | GEO
Project description:In this study, we used a cardiac-specific, inducible expression system to activate YAP in adult mouse heart. Activation of YAP in adult heart promoted cardiomyocyte proliferation and did not deleteriously affect heart function. Furthermore, YAP activation after myocardial infarction (MI) preserved heart function and reduced infarct size. Using adeno-associated virus subtype 9 (AAV9) as a delivery vector, we expressed human YAP in the murine myocardium immediately after MI. We found that AAV9:hYAP significantly improved cardiac function and mouse survival. AAV9:hYAP did not exert its salutary effects by reducing cardiomyocyte apoptosis. Rather, we found that AAV9:hYAP stimulated adult cardiomyocyte proliferation. Gene expression profiling indicated that AAV9:hYAP stimulated cell cycle gene expression, enhanced TGFβ-signaling, and activated of components of the inflammatory response.Cardiac specific YAP activation after MI mitigated myocardial injury after MI, improved cardiac function and mouse survival. These findings suggest that therapeutic activation of hYAP or its downstream targets, potentially through AAV-mediated gene therapy, may be a strategy to improve outcome after MI. Three groups were involved in this study: sham group, AAV9:Luci+MI group and AAV9-YAP+MI group. Each group contained three biological replicates. The sham group had neither myocardial infarction nor AAV injection. The AAV9:Luci +MI(L for brief) group had myocardial infarction and injected with AAV9:Luic. The AAV9:hYAP+MI(YAP for brief) group had myocardial infarction and injected with AAV9:hYAP. 5 days after MI and AAV injection, the heart apexes were collected and the total RNA were isolated for microarray analysis.
2014-05-26 | E-GEOD-54612 | biostudies-arrayexpress
Project description:Purpose: To uncover the molecular mechanisms underlying RBM22-mediated neonatal heart regeneration, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis on regenerative and non-regenerative wild-type (WT) mouse cardiomyocytes over a 7-day period. Methods: Cardiomyocytes were isolated from postnatal day 1 (P1, regenerative) and postnatal day 8 (P8, non-regenerative) mice, and cultured in DMEM supplemented with 10% fetal bovine serum at 37°C in a 5% CO₂ atmosphere. Cells were stained to confirm the expression of c-TnT, and only those with purity >97.5% were used for subsequent experiments.Results: We carried out a CUT&Tag assay using antibody against RBM22 and found the global influence of RBM22 in regulating genes in transcription regulatory regions of key genes involved in proliferative cardiomyocyte effector function.
2026-02-12 | GSE295697 | GEO
Project description:Promoting the proliferation of endogenous cardiomyocytes represents a promising strategy for treating cardiac injuries. Identifying key factors that regulate cardiomyocyte proliferation can advance the development of novel therapies for heart regeneration. Here we identify that FOXK1 and FOXK2 act as master regulators of cardiomyocyte proliferation and metabolism. The expression of FOXK1 and FOXK2 decreased with postnatal heart development. Cardiomyocyte-specific knockout of Foxk1 or Foxk2 inhibited neonatal heart regeneration after myocardial infarction (MI) injury. Conversely, AAV9-mediated cardiomyocyte-specific overexpression of FOXK1 or FOXK2 prolonged the postnatal proliferative window of cardiomyocytes and enhanced cardiac repair in adult mice by promoting endogenous cardiomyocyte proliferation after MI. Mechanistically, FOXK1 and FOXK2 induce Ccnb1 and Cdk1 transcription and cardiomyocyte cell cycle progression, respectively. Ccnb1 knockdown hindered FOXK1 overexpression-induced cardiomyocyte proliferation, and the same effect was observed when Cdk1 was knocked down in FOXK2 overexpressing cardiomyocytes. Additionally, we further revealed that FOXK1 and FOXK2 induced a metabolic shift toward glycolysis by promoting HIF1α expression in cardiomyocytes, which favors cardiomyocyte proliferation. Our findings identify FOXK1 and FOXK2 as critical triggers of cardiomyocyte proliferation and define these two transcription factors as novel therapeutic targets for myocardial infarction.
2025-02-13 | MTBLS12191 | MetaboLights
Project description:Coronary heart disease is a main cause of death in the developed world and treatment success remains modest with high mortality rates within one year after myocardial infarction (MI). Thus, new therapeutic targets and effective treatments are necessary. Short telomeres are risk factors for age-associated diseases including heart disease. Here, we address the potential of telomerase (Tert) activation in prevention of heart failure after MI in adult mice. We use adeno-associated viruses for cardiac-specific Tert expression in a mouse model of MI. We find that upon MI, hearts expressing Tert show attenuated cardiac dilation, improved ventricular function and smaller infarct scars concomitant with increased mouse survival by 17% compared to controls. Furthermore, Tert treatment results in elongated telomeres, increased numbers of Ki67 and pH3-positive cardiomyocytes and a gene expression switch towards a regeneration signature of neonatal mice. Our work highlights telomerase activation as a novel therapeutic strategy to prevent heart failure after MI. Mice of one year of age were left untreated (control) or injected with 5*10^11 adeno associated viruses particles of serotype 9 (AAV9) that carry either en empty expression cassette or express telomerase under control of the CMV promoter. Virus injected mice then underwent myocardial infarction induced through permenant left anterior descending artery (LAD) ligation. Mice that survived for six weeks after LAD ligation were sacrificed and 4 hearts per group (AAV9-empty or AAV9-Tert) and 3 control hearts (no virus treatment, no ligation) were subjected to total RNA isolation for micro array analysis.
2014-12-15 | E-GEOD-62973 | biostudies-arrayexpress
Project description:Aim: To determine RNA expression levels in heart tissues of mice 4 post Myc activation. Mice were either untreated or systemically infected with a cardiomyocyte specific adeno associated virus (AAV9) at 4 to 6 weeks of age. Cardiomyocytes were isolated from adult mice that were either untreated or infected with AAV9-CCNT1 and were either Myh6-cre;R26CAG-c-MycERT2/+ or R26CAG-c-MycERT2/+ following 4 hours of MycER activation via administration of (Z)-4-hydroxytamoxifen.
2020-02-24 | E-MTAB-8515 | biostudies-arrayexpress
Project description:In this study, we used a cardiac-specific, inducible expression system to activate YAP in adult mouse heart. Activation of YAP in adult heart promoted cardiomyocyte proliferation and did not deleteriously affect heart function. Furthermore, YAP activation after myocardial infarction (MI) preserved heart function and reduced infarct size. Using adeno-associated virus subtype 9 (AAV9) as a delivery vector, we expressed human YAP in the murine myocardium immediately after MI. We found that AAV9:hYAP significantly improved cardiac function and mouse survival. AAV9:hYAP did not exert its salutary effects by reducing cardiomyocyte apoptosis. Rather, we found that AAV9:hYAP stimulated adult cardiomyocyte proliferation. Gene expression profiling indicated that AAV9:hYAP stimulated cell cycle gene expression, enhanced TGFβ-signaling, and activated of components of the inflammatory response.Cardiac specific YAP activation after MI mitigated myocardial injury after MI, improved cardiac function and mouse survival. These findings suggest that therapeutic activation of hYAP or its downstream targets, potentially through AAV-mediated gene therapy, may be a strategy to improve outcome after MI.
2014-05-26 | GSE54612 | GEO
Project description:Aims: Cardiomyocytes apoptosis is the predominant pathological feature following myocardial infarction (MI) and significantly impacts disease progression and outcomes. Zinc finger NFX1-type containing 1 (ZNFX1), an RNA helicase family member, remains relatively understudied in molecular biology and its role in cardiovascular diseases remains unclear. This study aims to explore the involvement of ZNFX1 in MI and uncover its mechanisms underlying cardiomyocyte apoptosis. Methods and results: Male C57BL/6 mice were administered AAV9-ZNFX1 or AAV9-sh-ZNFX1 with the cTNT promoter via tail vein injection for the purpose of cardiomyocyte-specific ZNFX1 overexpression or knockdown. Concurrently, left anterior descending coronary artery ligation (LAD) was performed to induce MI. Echocardiography was utilized to evaluate the cardiac function. Triphenyl tetrazolium chloride (TTC), Hematoxylin and eosin (HE) and Masson's trichrome staining were used to evaluate the cardiac infarction and cardiac remodeling. TUNEL assay, flow cytometry, western blot and quantitative reverse transcription PCR (qRT-PCR) were employed to evaluate apoptosis. The cardiomyocyte viability was quantified using the CCK-8 assay. RNA sequencing (RNA-seq) and RNA immunoprecipitation assays (RIP) were employed to investigate the interaction between ZNFX1 and apoptosis-associated genes. The expression of ZNFX1 was decreased in MI myocardium and hypoxia-treated cardiomyocytes. Overexpression of ZNFX1 significantly attenuated cardiac dysfunction, reduced infarct size, inhibited collagen deposition and alleviated cardiac hypertrophy which was ascribed to MI in mice, whereas knockdown of ZNFX1 produced the opposite effects. RNA-seq identified apoptosis as a possible regulated pathway of ZNFX1, overexpression of ZNFX1 represses the cardiomyocyte apoptosis that gives rise to MI while knockdown of ZNFX1 deteriorates it. Mechanically, ZNFX1 binds with mRNA of apoptosis genes that contain highly structured 3'UTR and prompts their decay. Conclusion: ZNFX1 plays a protective role in MI by degrading mRNA of apoptosis-related genes, which often possess highly structured 3'UTRs. This highlights ZNFX1 as a potential novel molecular target for treating cardiac dysfunction associated with MI. Keywords: ZNFX1, apoptosis, mRNA stability, helicase activity, UPF1, myocardial infarction
2025-06-25 | GSE273385 | GEO
Project description:Aims: Cardiomyocytes apoptosis is the predominant pathological feature following myocardial infarction (MI) and significantly impacts disease progression and outcomes. Zinc finger NFX1-type containing 1 (ZNFX1), an RNA helicase family member, remains relatively understudied in molecular biology and its role in cardiovascular diseases remains unclear. This study aims to explore the involvement of ZNFX1 in MI and uncover its mechanisms underlying cardiomyocyte apoptosis. Methods and results: Male C57BL/6 mice were administered AAV9-ZNFX1 or AAV9-sh-ZNFX1 with the cTNT promoter via tail vein injection for the purpose of cardiomyocyte-specific ZNFX1 overexpression or knockdown. Concurrently, left anterior descending coronary artery ligation (LAD) was performed to induce MI. Echocardiography was utilized to evaluate the cardiac function. Triphenyl tetrazolium chloride (TTC), Hematoxylin and eosin (HE) and Masson's trichrome staining were used to evaluate the cardiac infarction and cardiac remodeling. TUNEL assay, flow cytometry, western blot and quantitative reverse transcription PCR (qRT-PCR) were employed to evaluate apoptosis. The cardiomyocyte viability was quantified using the CCK-8 assay. RNA sequencing (RNA-seq) and RNA immunoprecipitation assays (RIP) were employed to investigate the interaction between ZNFX1 and apoptosis-associated genes. The expression of ZNFX1 was decreased in MI myocardium and hypoxia-treated cardiomyocytes. Overexpression of ZNFX1 significantly attenuated cardiac dysfunction, reduced infarct size, inhibited collagen deposition and alleviated cardiac hypertrophy which was ascribed to MI in mice, whereas knockdown of ZNFX1 produced the opposite effects. RNA-seq identified apoptosis as a possible regulated pathway of ZNFX1, overexpression of ZNFX1 represses the cardiomyocyte apoptosis that gives rise to MI while knockdown of ZNFX1 deteriorates it. Mechanically, ZNFX1 binds with mRNA of apoptosis genes that contain highly structured 3'UTR and prompts their decay. Conclusion: ZNFX1 plays a protective role in MI by degrading mRNA of apoptosis-related genes, which often possess highly structured 3'UTRs. This highlights ZNFX1 as a potential novel molecular target for treating cardiac dysfunction associated with MI. Keywords: ZNFX1, apoptosis, mRNA stability, helicase activity, UPF1, myocardial infarction
2025-06-25 | GSE272829 | GEO