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Exploring Heart Failure Through Bioinformatics: A Transcriptomic Analysis of Cardiac and Adipose Tissues
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Department of Cell and Molecular Biology.ORCID iD: 0000-0003-1445-0347
2025 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
Abstract [en]

Heart failure, characterised by either preserved (HFpEF) or reduced (HFrEF) left ventricular ejection fraction, involves complex and diverse pathophysiological mechanisms, making it a challenging field of research. Despite extensive studies, much remains to be learned about its underlying mechanisms and early diagnostic markers—particularly for HFpEF, as evidenced by the lack of effective treatment options.

This thesis aims to explore the transcriptomic profiles of cardiac and adipose tissues in patients with different HF phenotypes, investigating differential gene expression, associated regulatory pathways, and correlation networks. Additionally, the work examines the expression of specific genes involved in iron metabolism under conditions of iron deficiency in myocardial and skeletal muscle tissues.

Using high-throughput RNA sequencing, gene expression was analyzed in left and right ventricular biopsies from patients undergoing coronary artery bypass grafting, with or without diagnostic signs of HF. Gene expression and network analysis techniques were employed to identify distinct gene expression patterns and potential regulatory mechanisms in epicardial adipose tissue.

The studies revealed significant differences in gene expression related to myocardial contraction, energy supply, remodeling, and fibrosis between HFpEF and normal physiology, as well as distinct profiles between HFpEF and HFrEF. Moreover, genes involved in heart muscle movement and energy production were less active in the left ventricle of HFpEF, particularly those facilitating contraction and relaxation of the heart muscle. This reduced activity potentially explains the stiffness and impaired relaxation characteristic of HFpEF. Additionally, genes influencing the heart's structural integrity, especially those involved in collagen production, showed changes that suggest alterations beyond simple stiffening in the heart’s structure. The analysis of adipose tissues identified unique gene expression clusters correlating with echocardiographic HF characteristics. These findings reveal the pathophysiological discrepancies and shared mechanisms across HF subtypes, offering a richer understanding of the disease's transcriptomic basis.

By demonstrating the distinct transcriptomic signatures associated with HFpEF and HFrEF, this thesis builds on our understanding of heart failure's complex biology. Further research is needed to explore the therapeutic potential of the identified targets and to validate these findings in a larger, but also a more diverse patient cohort.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2025. , p. 79
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2514
Keywords [en]
Transcriptomics, NGS, Heart Failure, HFpEF, HFrEF, Ischemic heart disease, Left ventricle dysfunction, Gene Expression, RNA Sequencing, Cardiac Biopsy, Epicaridal adipose tissue
National Category
Bioinformatics and Computational Biology
Identifiers
URN: urn:nbn:se:uu:diva-552529ISBN: 978-91-513-2421-0 (print)OAI: oai:DiVA.org:uu-552529DiVA, id: diva2:1944787
Public defence
2025-05-07, room A1:107a, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2025-04-14 Created: 2025-03-16 Last updated: 2025-04-14
List of papers
1. Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction
Open this publication in new window or tab >>Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction
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2019 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 3179Article in journal (Refereed) Published
Abstract [en]

Heart failure affects 2-3% of adult Western population. Prevalence of heart failure with preserved left ventricular (LV) ejection fraction (HFpEF) increases. Studies suggest HFpEF patients to have altered myocardial structure and functional changes such as incomplete relaxation and increased cardiac stiffness. We hypothesised that patients undergoing elective coronary bypass surgery (CABG) with HFpEF characteristics would show distinctive gene expression compared to patients with normal LV physiology. Myocardial biopsies for mRNA expression analysis were obtained from sixteen patients with LV ejection fraction >= 45%. Five out of 16 patients (31%) had echocardiographic characteristics and increased NTproBNP levels indicative of HFpEF and this group was used as HFpEF proxy, while 11 patients had Normal LV physiology. Utilising principal component analysis, the gene expression data clustered into two groups, corresponding to HFpEF proxy and Normal physiology, and 743 differentially expressed genes were identified. The associated top biological functions were cardiac muscle contraction, oxidative phosphorylation, cellular remodelling and matrix organisation. Our results also indicate that upstream regulatory events, including inhibition of transcription factors STAT4, SRF and TP53, and activation of transcription repressors HEY2 and KDM5A, could provide explanatory mechanisms to observed gene expression differences and ultimately cardiac dysfunction in the HFpEF proxy group.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Cardiology and Cardiovascular Disease
Identifiers
urn:nbn:se:uu:diva-379578 (URN)10.1038/s41598-019-39445-2 (DOI)000459897600113 ()30816197 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2019-04-12 Created: 2019-04-12 Last updated: 2025-03-16Bibliographically approved
2. Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure
Open this publication in new window or tab >>Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure
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2024 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 5811Article in journal (Refereed) Published
Abstract [en]

New or mild heart failure (HF) is mainly caused by left ventricular dysfunction. We hypothesised that gene expression differ between the left (LV) and right ventricle (RV) and secondly by type of LV dysfunction. We compared gene expression through myocardial biopsies from LV and RV of patients undergoing elective coronary bypass surgery (CABG). Patients were categorised based on LV ejection fraction (EF), diastolic function and NT-proBNP into pEF (preserved; LVEF ≥ 45%), rEF (reduced; LVEF < 45%) or normal LV function. Principal component analysis of gene expression displayed two clusters corresponding to LV and RV. Up-regulated genes in LV included natriuretic peptides NPPA and NPPB, transcription factors/coactivators STAT4 and VGLL2, ion channel related HCN2 and LRRC38 associated with cardiac muscle contraction, cytoskeleton, and cellular component movement. Patients with pEF phenotype versus normal differed in gene expression predominantly in LV, supporting that diastolic dysfunction and structural changes reflect early LV disease in pEF. DKK2 was overexpressed in LV of HFpEF phenotype, potentially leading to lower expression levels of β-catenin, α-SMA (smooth muscle actin), and enhanced apoptosis, and could be a possible factor in the development of HFpEF. CXCL14 was down-regulated in both pEF and rEF, and may play a role to promote development of HF.

Place, publisher, year, edition, pages
Springer Nature, 2024
Keywords
Heart failure, Ischemic heart disease, Cardiac biopsy, Left ventricular dysfunction, Gene expression
National Category
Cardiology and Cardiovascular Disease
Identifiers
urn:nbn:se:uu:diva-531587 (URN)10.1038/s41598-024-56025-1 (DOI)001185505600023 ()38461325 (PubMedID)
Funder
Swedish Research Council, 2018-0899Swedish Research Council, 2020-01978Knut and Alice Wallenberg FoundationScience for Life Laboratory, SciLifeLab, 1377AstraZeneca, 1377eSSENCE - An eScience CollaborationUppsala UniversitySwedish National Infrastructure for Computing (SNIC)UPPMAX
Available from: 2024-06-18 Created: 2024-06-18 Last updated: 2025-03-16Bibliographically approved
3. Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting
Open this publication in new window or tab >>Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting
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2024 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 25, no 1, article id 938Article in journal (Refereed) Published
Abstract [en]

Background

Epicardial adipose tissue (EAT) surrounds the heart and is hypothesised to play a role in the development of heart failure (HF). In this study, we first investigated the differences in gene expression between epicardial adipose tissue (EAT) and subcutaneous adipose tissue (SAT) in patients undergoing elective coronary artery bypass graft (CABG) surgery (n = 21; 95% male). Secondly, we examined the association between EAT and SAT in patients at risk for HF stage A (n = 12) and in pre-HF patients, who show signs but not symptoms of HF, stage B (n = 9).

Results

The study confirmed a distinct separation between EAT and SAT. In EAT 17 clusters of genes were present, of which several novel gene modules are associated with characteristics of HF. Notably, seven gene modules showed significant correlation to measures of HF, such as end diastolic left ventricular posterior wall thickness, e’mean, deceleration time and BMI. One module was particularly distinct in EAT when compared to SAT, featuring key genes such as FLT4, SEMA3A, and PTX3, which are implicated in angiogenesis, inflammation regulation, and tissue repair, suggesting a unique role in EAT linked to left ventricular dysfunction. Genetic expression was compared in EAT across all pre-HF and normal phenotypes, revealing small genetic changes in the form of 18 differentially expressed genes in ACC/AHA Stage A vs. Stage B.

Conclusions

The roles of subcutaneous and epicardial fat are clearly different. We highlight the gene expression difference in search of potential modifiers of HF progress. The true implications of our findings should be corroborated in other studies since HF ACC/AHA stage B patients are common and carry a considerable risk for progression to symptomatic HF.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2024
Keywords
Epicardial adipose tissue, Gene expression, Weighted gene cluster, Heart failure, Bioinformatics
National Category
Cardiology and Cardiovascular Disease
Identifiers
urn:nbn:se:uu:diva-541307 (URN)10.1186/s12864-024-10851-9 (DOI)001330563200001 ()39375631 (PubMedID)
Funder
Swedish Research Council, 2020-01978Knut and Alice Wallenberg FoundationeSSENCE - An eScience CollaborationUppsala UniversityScience for Life Laboratory, SciLifeLabSwedish National Infrastructure for Computing (SNIC)UPPMAX
Available from: 2024-10-30 Created: 2024-10-30 Last updated: 2025-03-16Bibliographically approved
4. Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle
Open this publication in new window or tab >>Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle
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2023 (English)In: International Journal of Cardiology, ISSN 0167-5273, E-ISSN 1874-1754, Vol. 379, p. 82-88Article in journal (Refereed) Published
Abstract [en]

Background: Iron deficiency (ID) is associated with adverse prognosis in patients with heart failure. This study aims to investigate the relationship between ID and expression of genes involved in iron metabolism in human myocardium and skeletal muscle, focusing on Transferrin 1 receptor (TfR1), the main pathway of cellular iron uptake.

Methods: Patients undergoing elective CABG were assessed prior to surgery with echocardiography and serum iron parameters. Core needle biopsies were collected from the left and right ventricle (LV, RV), the right atrium and intercostal skeletal muscle (SM). Gene expression analyses were done by mRNA sequencing.

Results: Of 69 patients (median age 69 years, 91% men), 28% had ID. 26% had HFrEF, 25% had HFpEF phys-iology according to echocardiographic findings and NT-proBNP levels, and 49% had normal LV function. The expression of TfR1 was increased in patients with ID compared to patients without ID in ventricular tissue (p = 0.04) and in intercostal SM (p = 0.01). The increase in TfR1 expression in LV and RV was more pronounced when analysing patients with absolute ID (S-Ferritin<100 mu g/L). Analysing the correlation between various iron pa-rameters, S-Ferritin levels showed the strongest correlation with TfR1 expression. There was no correlation with NT-proBNP levels and no difference in TfR1 expression between different HF phenotypes.

Conclusions: In patients undergoing elective CABG we found an association between ID and increased TfR1 expression in myocardium regardless of LV function, indicating physiologically upregulated TfR1 expression in the presence of ID to restore intracellular iron needs.

Place, publisher, year, edition, pages
ElsevierELSEVIER IRELAND LTD, 2023
Keywords
Iron deficiency, Heart failure, Iron metabolism, Myocardial metabolism
National Category
Cardiology and Cardiovascular Disease
Identifiers
urn:nbn:se:uu:diva-502664 (URN)10.1016/j.ijcard.2023.03.032 (DOI)000979249700001 ()36931398 (PubMedID)
Funder
Stockholm County CouncilKarolinska InstituteAstraZeneca, 1377
Available from: 2023-05-31 Created: 2023-05-31 Last updated: 2025-03-16Bibliographically approved

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