A Cost-Effective Nuclei Isolation Protocol for Single Nucleus RNA-Sequencing of Mouse HFpEF Hearts
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE331341 | GEO | 2026/09/12
REPOSITORIES: GEO
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Project description:A Cost-Effective Nuclei Isolation Protocol for Single Nucleus RNA-Sequencing of Mouse HFpEF Hearts
| PRJNA1467710 | ENA
Project description:Background: Heart failure with preserved ejection fraction (HFpEF) constitutes more than half of all heart failure but has few effective therapies. Recent human myocardial transcriptomics and metabolomics have revealed major differences between HFpEF, HF with reduced EF (HFrEF), and controls. How this translates at the protein level is currently unknown. Methods: Myocardial tissue from patients with HFpEF and non-failing donor controls was analyzed by data-dependent (DDA, n=10 HFpEF, n=9 controls) and data-independent (DIA, n=44 HFpEF, n=5 controls) mass spectrometry-based proteomics. Previously reported myocardial proteomic data from end-stage HFrEF and controls were also used. Differential protein expression analysis, machine learning and pathway enrichment were integrated with clinical characteristics and myocardial transcriptomics. Results: DDA-MS proteomics identified 88 significantly upregulated and 248 down-regulated proteins in HFpEF vs controls, out of 1996 identified proteins. Principal component analysis of DDA-MS proteomics found HFpEF was separated into 2 sub-groups: one being similar to controls the other quite disparate. Top proteins contributing to the separation of HFpEF subgroups were enriched in actin/myosin binding, regulation of DNA replication/repair, transcription, and translation. Downregulated proteins in HFpEF vs controls were enriched in pathways related to ribosome structure, transmembrane transporters, metabolic enzymes, and oxidative phosphorylation (OxPhos) proteins. Enriched pathways for proteins upregulated in HFpEF related to actin and phospholipid binding, growth factor signaling, kinase regulation, and glycolysis. Ingenuity pathway analysis predicted downregulation of protein translation, mitochondrial function, and glucose and fat metabolism in HFpEF. OxPhos gene (increased) versus protein (decreased) expression was discordant in HFpEF. The second DIA proteomic analysis also yielded two HFpEF sub-groups; the one most different from controls also having reduced OxPhos and protein translation pathways. A higher proportion of these patients also had severe obesity. Conclusions: Integrative proteomics, transcriptomics, and pathway analysis supports a translational defect particularly involving mitochondrial, ribosomal and protein translation proteins in HFpEF. Patients with more distinct proteomic signatures from control were more often very obese. The results support therapeutic efforts targeting metabolism, mitochondrial function, and protein translation in this subgroup.
2024-03-05 | PXD045677 | Pride
Project description:In this project we explore the cellular heterogeneity of a mouse model of heart failure with preserved ejection fraction (HFpEF) involving a two-hit model of feeding a high fat diet (HFD) along with L-NAME administration. Healthy adult male mice (C57BL/6J inbred) were fed either a normal chow diet or HFD/L-NAME for 10 weeks or 15 weeks before performing sequencing experiments. Both cardiomyocytes (CMs) and total interstitial population (TIP) were captured using a protocol to jointly capture and sequence single-nuclei (for cardiomyocytes) and single-cells (for TIP) using the 10x Genomics Chromium system.
2024-05-08 | E-MTAB-13362 | biostudies-arrayexpress
Project description:HFpEF mouse model was established by a \"double hit\" of L-NAME and high-fat diet (60% fat). 5-week-old C57BL/6N mice were given the above intervention for 5 weeks (Early HFpEF group) or 12 weeks (Advanced HFpEF group). 17-week-old mice fed a normal diet were used as the Control group. After adequate perfusion, the hearts were harvested. Ventricular RNA was extracted for RNA sequencing.
2025-12-31 | E-MTAB-15255 | biostudies-arrayexpress
Project description:Heart failure with preserved ejection fraction (HFpEF) accounts for half of heart failure cases and is characterised by reduced pericyte coverage. While the contributions of other cardiac cell types to HFpEF are well-studied, the role of pericytes remains less understood. Using murine single-nucleus RNA sequencing to study cardiac pericytes in HFpEF, we identified reduced STAT3 expression as a hallmark of HFpEF pericytes. Mechanistic studies in vitro revealed that STAT3 deletion induces cellular senescence and impairs pericyte adhesion, recapitulating HFpEF-like characteristics. These findings suggest that STAT3 is crucial for maintaining pericyte homeostasis and highlight its reduction as a potential driver of pericyte loss, a defining feature of HFpEF.
2025-04-25 | E-MTAB-15019 | biostudies-arrayexpress
Project description:Background: HFpEF is a heterogeneous clinical picture that is closely related to extracardiac comorbidities such as obesity, hypertension and diabetes and is associated with chronic, low-grade systemic inflammation. Previous studies on myocardial biopsies of HFpEF patients showed intramyocardial inflammatory activity, suggesting that the inflammatory processes in HFpEF are predominantly systemic and exhibit compartment specific-patterns. Methods: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) of HFpEF patients (n=6), HFrEF patients (n=8) and healthy controls (n=7) taking obesity status into account. For validation, bulk RNA sequencing was performed on whole blood samples. In parallel, the systemic immune cell response was investigated in a HFpEF mouse model (induced by a high-fat diet plus L-NAME), with one group additionally administered the anti-inflammatory agent nitro-oleic acid (NO₂-OA). Results: Analysis of human PBMCs revealed a HFpEF-specific inflammatory fingerprint, which manifested in obesity-related increased expression of cytokine signaling genes (e.g. CCL2, TNF) and obesity-independent increases in mitochondrial-associated activity. In the mouse model, HFpEF animals showed a comparable increase in inflammatory markers, with treatment with NO₂-OA leading to a partial normalization of immunological signatures and a significant improvement in diastolic function. Conclusion: Our results demonstrate that the immune cells of patients with HFpEF are characterized by a distinct transcriptional immune signature that differs from that of patients with HFrEF. The conserved immunological signatures between humans and mice, and the beneficial effect of NO₂-OA in a preclinical model, provide important translational insights and generate hypotheses for personalized interventions in HFpEF.
2025-07-28 | GSE298173 | GEO
Project description:Background: HFpEF is a heterogeneous clinical picture that is closely related to extracardiac comorbidities such as obesity, hypertension and diabetes and is associated with chronic, low-grade systemic inflammation. Previous studies on myocardial biopsies of HFpEF patients showed intramyocardial inflammatory activity, suggesting that the inflammatory processes in HFpEF are predominantly systemic and exhibit compartment specific-patterns. Methods: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) of HFpEF patients (n=6), HFrEF patients (n=8) and healthy controls (n=7) taking obesity status into account. For validation, bulk RNA sequencing was performed on whole blood samples. In parallel, the systemic immune cell response was investigated in a HFpEF mouse model (induced by a high-fat diet plus L-NAME), with one group additionally administered the anti-inflammatory agent nitro-oleic acid (NO₂-OA). Results: Analysis of human PBMCs revealed a HFpEF-specific inflammatory fingerprint, which manifested in obesity-related increased expression of cytokine signaling genes (e.g. CCL2, TNF) and obesity-independent increases in mitochondrial-associated activity. In the mouse model, HFpEF animals showed a comparable increase in inflammatory markers, with treatment with NO₂-OA leading to a partial normalization of immunological signatures and a significant improvement in diastolic function. Conclusion: Our results demonstrate that the immune cells of patients with HFpEF are characterized by a distinct transcriptional immune signature that differs from that of patients with HFrEF. The conserved immunological signatures between humans and mice, and the beneficial effect of NO₂-OA in a preclinical model, provide important translational insights and generate hypotheses for personalized interventions in HFpEF.
2025-07-28 | GSE298172 | GEO
Project description:Background: HFpEF is a heterogeneous clinical picture that is closely related to extracardiac comorbidities such as obesity, hypertension and diabetes and is associated with chronic, low-grade systemic inflammation. Previous studies on myocardial biopsies of HFpEF patients showed intramyocardial inflammatory activity, suggesting that the inflammatory processes in HFpEF are predominantly systemic and exhibit compartment specific-patterns. Methods: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) of HFpEF patients (n=6), HFrEF patients (n=8) and healthy controls (n=7) taking obesity status into account. For validation, bulk RNA sequencing was performed on whole blood samples. In parallel, the systemic immune cell response was investigated in a HFpEF mouse model (induced by a high-fat diet plus L-NAME), with one group additionally administered the anti-inflammatory agent nitro-oleic acid (NO₂-OA). Results: Analysis of human PBMCs revealed a HFpEF-specific inflammatory fingerprint, which manifested in obesity-related increased expression of cytokine signaling genes (e.g. CCL2, TNF) and obesity-independent increases in mitochondrial-associated activity. In the mouse model, HFpEF animals showed a comparable increase in inflammatory markers, with treatment with NO₂-OA leading to a partial normalization of immunological signatures and a significant improvement in diastolic function. Conclusion: Our results demonstrate that the immune cells of patients with HFpEF are characterized by a distinct transcriptional immune signature that differs from that of patients with HFrEF. The conserved immunological signatures between humans and mice, and the beneficial effect of NO₂-OA in a preclinical model, provide important translational insights and generate hypotheses for personalized interventions in HFpEF.
2025-07-28 | GSE298171 | GEO
Project description:To investigate gene expression changes associated with the development of HFpEF and the preventive effects of pharmacological interventions against HFpEF onset, Wistar rats were administered N(G)-Nitro-L-arginine methyl ester, an inhibitor of nitric oxide synthase, and fed a high-fat diet for 8 weeks. Cardiac tissues were collected at the time of sacrifice.
2025-12-01 | GSE297653 | GEO
Project description:Background: Heart failure with preserved ejection fraction (HFpEF) is increasingly acknowledged as a major public health concern due to its complex pathophysiology that involves neuroinflammation and sympathetic activation. The crosstalk between the heart and hypothalamic microglia in HFpEF, particularly the role of small extracellular vesicles (sEVs), remains insufficiently explored. Methods and Results: We constructed a HFpEF model in mice by combining a long-term high-fat diet with the nitric oxide synthase inhibitor L-NAME. These mice exhibited activation of microglia and hypothalamic inflammation. Microglia depletion with PLX3397 suppressed sympathetic activity and improved cardiac dysfunction in HFpEF. sEVs derived from the myocardium of HFpEF mice induced a pro-inflammatory M1 phenotype in microglia, leading to hypothalamic inflammation and sympathetic activation. Intraperitoneal injection of the sEVs biogenesis inhibitor GW4869 reversed these changes in HFpEF mice. Similar pathological changes were observed in BV2 microglia treated with sEVs isolated from palmitic acid-treated HL-1 cardiomyocytes. Bioinformatic and RT-qPCR analyses revealed a notable upregulation of miR-200c-3p in sEVs derived from both HFpEF myocardial tissue and palmitic acid- treated HL-1 cardiomyocytes, as well as in microglia. Cardiomyocyte-specific miR-200c-3p sponge inhibited microglial activation, hypothalamic inflammation and sympathetic activation in HFpEF mice. Conversely, miR-200c-3p mimic exacerbated pro-inflammatory responses in BV2, while miR-200c-3p inhibitor prevented the transition to a pro-inflammatory phenotype. The anti-inflammatory protein DUSP1 was validated as a potential downstream target of miR-200c-3p in microglia. Conclusions: Our study reveals that HFpEF prompts cardiomyocytes to release sEVs enriched with miR-200c-3p, leading to hypothalamic inflammation and evoking sympathetic outflow, which in turn exacerbates cardiac dysfunction. Focusing on sEV-mediated communication between cardiomyocytes and microglia may offer a new therapeutic approach for HFpEF.
2026-07-01 | GSE334160 | GEO