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Molecular Advances in Heart Disease: Genomics, Proteomics, and Bioinformatics of Heart Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: 20 May 2025 | Viewed by 6113

Special Issue Editor

Dr. Justyna Fert-Bober

E-Mail Website
Guest Editor
Cedars-Sinai Medical Center, Cedars-Sinai, 127 San Vicente Blvd #A9100, Los Angeles, CA 90048, USA
Interests: cardiovascular disease; cardiac fibrosis; peptidylarginine deiminase; citrullination; posttranslational modifications

Special Issue Information

Dear Colleagues,

We are welcoming submissions for our new Special Issue titled Molecular Advances in Heart Disease. This Special Issue aims to present publications that elucidate heart disease’s etiology and pathophysiology. We will accept articles focusing on the study and interpretation of molecular, genetic, proteomic, and metabolomic changes in tissues and cells to aid in the diagnosis, pathogenesis, prognosis, and treatment of heart diseases. In addition to basic science, we welcome translational research and clinical evidence that supports biomolecular experiments. Every year, approximately 647,000 Americans die from heart disease, which is 1 in every 4 deaths, making it the leading cause of death and an important unmet medical need. We hope that this Special Issue will collate papers that foster a comprehensive understanding of this condition and breakthroughs in the field of heart disease research.

Dr. Justyna Fert-Bober
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • heart disease
  • cardiovascular disease
  • coronary artery disease (CAD)
  • heart attack
  • heart failure
  • arrhythmia (abnormal heart rhythms)
  • valve disease
  • high blood pressure
  • congenital heart conditions
  • inherited heart conditions
  • fibrosis
  • pathobiology of fibrosis
  • aging
  • chronic inflammation
  • inflammatory and cardiovascular diseases
  • myocarditis
  • extracellular matrix biology

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Published Papers (4 papers)

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Research

25 pages, 5062 KiB  
Article
Genome-Wide Expression Profiling and Phenotypic Analysis of Downstream Targets Identify the Fox Transcription Factor Jumeau as a Master Regulator of Cardiac Progenitor Cell Division
by M. Rezaul Hasan, Andrew J. Kump, Evelyn C. Stepaniak, Manoj Panta, Kuncha Shashidhar, Rajnandani Katariya, Mofazzal K. Sabbir, Kristopher R. Schwab, Mark H. Inlow, Ye Chen and Shaad M. Ahmad
Int. J. Mol. Sci. 2024, 25(23), 12933; https://doi.org/10.3390/ijms252312933 - 1 Dec 2024
Viewed by 1701
Abstract
Forkhead box (Fox) transcription factors (TFs) mediate multiple conserved cardiogenic processes in both mammals and Drosophila. Our prior work identified the roles of two Drosophila Fox genes, jumeau (jumu) and Checkpoint suppressor 1-like (CHES-1-like), in cardiac progenitor cell [...] Read more.
Forkhead box (Fox) transcription factors (TFs) mediate multiple conserved cardiogenic processes in both mammals and Drosophila. Our prior work identified the roles of two Drosophila Fox genes, jumeau (jumu) and Checkpoint suppressor 1-like (CHES-1-like), in cardiac progenitor cell specification and division, and in the proper positioning of cardiac cell subtypes. Fox TF binding sites are also significantly enriched in the enhancers of genes expressed in the heart, suggesting that these genes may play a core regulatory role in one or more of these cardiogenic processes. We identified downstream targets of Jumu by comparing transcriptional expression profiles of flow cytometry-sorted mesodermal cells from wild-type embryos and embryos completely lacking the jumu gene and found that genes with functional annotation and ontological features suggesting roles in cell division were overrepresented among Jumu targets. Phenotypic analysis of a subset of these targets identified 21 jumu-regulated genes that mediate cardiac progenitor cell division, one of which, Retinal Homeobox (Rx), was characterized in more detail. Finally, the observation that many of these 21 genes and/or their orthologs exhibit genetic or physical interactions among themselves indicates that Jumu is a master regulator acting as a hub of a cardiac progenitor cell division-mediating network. Full article
(This article belongs to the Special Issue Molecular Advances in Heart Disease: Genomics, Proteomics, and Bioinformatics of Heart Research)
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16 pages, 1946 KiB  
Article
Bioinformatic Multi-Strategy Profiling of Congenital Heart Defects for Molecular Mechanism Recognition
by Fabyanne Guimarães de Oliveira, João Vitor Pacheco Foletto, Yasmin Chaves Scimczak Medeiros, Lavínia Schuler-Faccini and Thayne Woycinck Kowalski
Int. J. Mol. Sci. 2024, 25(22), 12052; https://doi.org/10.3390/ijms252212052 - 9 Nov 2024
Viewed by 1076
Abstract
Congenital heart defects (CHDs) rank among the most common birth defects, presenting diverse phenotypes. Genetic and environmental factors are critical in molding the process of cardiogenesis. However, these factors’ interactions are not fully comprehended. Hence, this study aimed to identify and characterize differentially [...] Read more.
Congenital heart defects (CHDs) rank among the most common birth defects, presenting diverse phenotypes. Genetic and environmental factors are critical in molding the process of cardiogenesis. However, these factors’ interactions are not fully comprehended. Hence, this study aimed to identify and characterize differentially expressed genes involved in CHD development through bioinformatics pipelines. We analyzed experimental datasets available in genomic databases, using transcriptome, gene enrichment, and systems biology strategies. Network analysis based on genetic and phenotypic ontologies revealed that EP300, CALM3, and EGFR genes facilitate rapid information flow, while NOTCH1, TNNI3, and SMAD4 genes are significant mediators within the network. Differential gene expression (DGE) analysis identified 2513 genes across three study types, (1) Tetralogy of Fallot (ToF); (2) Hypoplastic Left Heart Syndrome (HLHS); and (3) Trisomy 21/CHD, with LYVE1, PLA2G2A, and SDR42E1 genes found in three of the six studies. Interaction networks between genes from ontology searches and the DGE analysis were evaluated, revealing interactions in ToF and HLHS groups, but none in Trisomy 21/CHD. Through enrichment analysis, we identified immune response and energy generation as some of the relevant ontologies. This integrative approach revealed genes not previously associated with CHD, along with their interactions and underlying biological processes. Full article
(This article belongs to the Special Issue Molecular Advances in Heart Disease: Genomics, Proteomics, and Bioinformatics of Heart Research)
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16 pages, 1886 KiB  
Article
The Yield of Genetic Testing and Putative Genetic Factors of Disease Heterogeneity in Long QT Syndrome Patients
by Anna Bukaeva, Alexandra Ershova, Maria Kharlap, Anna Kiseleva, Vladimir Kutsenko, Evgeniia Sotnikova, Mikhail Divashuk, Maria Pokrovskaya, Elizaveta Garbuzova, Anastasia Blokhina, Oksana Kopylova, Evgenia Zotova, Anna Petukhova, Anastasia Zharikova, Vasily Ramensky, Marija Zaicenoka, Yuri Vyatkin, Alexey Meshkov and Oxana Drapkina
Int. J. Mol. Sci. 2024, 25(22), 11976; https://doi.org/10.3390/ijms252211976 - 7 Nov 2024
Viewed by 965
Abstract
Genetic overdiagnosis of long QT syndrome (LQTS) becomes a critical concern due to the high clinical significance of DNA diagnosis. Current guidelines for LQTS genetic testing recommend a limited scope and strict referral based on the Schwartz score. Nevertheless, LQTS may be underdiagnosed [...] Read more.
Genetic overdiagnosis of long QT syndrome (LQTS) becomes a critical concern due to the high clinical significance of DNA diagnosis. Current guidelines for LQTS genetic testing recommend a limited scope and strict referral based on the Schwartz score. Nevertheless, LQTS may be underdiagnosed in patients with borderline phenotypes. We aimed to evaluate the total yield of rare variants in cardiac genes in LQTS patients. The cohort of 82 patients with LQTS referral diagnosis underwent phenotyping, Schwartz score counting, and exome sequencing. We assessed known LQTS genes for diagnostics, as per guidelines, and a broader set of genes for research. Diagnostic testing yield reached 75% in index patients; all causal variants were found in KCNQ1, KCNH2, and SCN5A genes. Research testing of 248 heart-related genes achieved a 50% yield of molecular diagnosis in patients with a low Schwartz score (<3.5). In patients with LQTS-causing variants, each additional rare variant in heart-related genes added 0.94 points to the Schwartz score (p value = 0.04), reflecting the more severe disease in such patients than in those with causal variants but without additional findings. We conclude that the current LQTS genetic diagnosis framework is highly specific but may lack sensitivity for patients with a Schwartz score <3.5. Improving referral criteria for these patients could enhance DNA diagnosis. Also, our results suggest that additional variants in cardiac genes may affect the severity of the disease in the carriers of LQTS-causing variants, which may aid in identifying new modifier genes. Full article
(This article belongs to the Special Issue Molecular Advances in Heart Disease: Genomics, Proteomics, and Bioinformatics of Heart Research)
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12 pages, 1826 KiB  
Communication
Postmortem-Derived Exosomal MicroRNA 486-5p as Potential Biomarkers for Ischemic Heart Disease Diagnosis
by So-Yeon Kim, Sookyoung Lee, Jong-Tae Park, Su-Jin Lee and Hyung-Seok Kim
Int. J. Mol. Sci. 2024, 25(17), 9619; https://doi.org/10.3390/ijms25179619 - 5 Sep 2024
Viewed by 1009
Abstract
Exosomes are nanovesicles 30–150 nm in diameter released extracellularly. Those isolated from human body fluids reflect the characteristics of their cells or tissues of origin. Exosomes carry extensive biological information from their parent cells and have significant potential as biomarkers for disease diagnosis [...] Read more.
Exosomes are nanovesicles 30–150 nm in diameter released extracellularly. Those isolated from human body fluids reflect the characteristics of their cells or tissues of origin. Exosomes carry extensive biological information from their parent cells and have significant potential as biomarkers for disease diagnosis and prognosis. However, there are limited studies utilizing exosomes in postmortem diagnostics. In this study, we extended our initial research which identified the presence and established detection methodologies for exosomes in postmortem fluids. We analyzed exosomal miRNA extracted from plasma and pericardial fluid samples of a control group (n = 13) and subjects with acute myocardial infarction (AMI; n = 24). We employed next-generation sequencing (NGS) to investigate whether this miRNA could serve as biomarkers for coronary atherosclerosis leading to acute myocardial infarction. Our analysis revealed 29 miRNAs that were differentially expressed in the AMI group compared to the control group. Among these, five miRNAs exhibited more than a twofold increase in expression across all samples from the AMI group. Specifically, miR-486-5p levels were significantly elevated in patients with high-grade (type VI or above) atherosclerotic plaques, as per the American Heart Association criteria, highlighting its potential as a predictive biomarker for coronary atherosclerosis progression. Our results indicate that postmortem-derived exosomal microRNAs can serve as potential biomarkers for various human diseases, including cardiovascular disorders. This finding has profound implications for forensic diagnostics, a field critically lacking diagnostic markers. Full article
(This article belongs to the Special Issue Molecular Advances in Heart Disease: Genomics, Proteomics, and Bioinformatics of Heart Research)
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