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Zhang L, Ma Y, Li Q, Long Z, Zhang J, Zhang Z, Qin X. Construction of a novel lower-extremity peripheral artery disease subtype prediction model using unsupervised machine learning and neutrophil-related biomarkers. Heliyon 2024; 10:e24189. [PMID: 38293541 PMCID: PMC10827514 DOI: 10.1016/j.heliyon.2024.e24189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Lower-extremity peripheral artery disease (LE-PAD) is a prevalent circulatory disorder with risks of critical limb ischemia and amputation. This study aimed to develop a prediction model for a novel LE-PAD subtype to predict the severity of the disease and guide personalized interventions. Additionally, LE-PAD pathogenesis involves altered immune microenvironment, we examined the immune differences to elucidate LE-PAD pathogenesis. A total of 460 patients with LE-PAD were enrolled and clustered using unsupervised machine learning algorithms (UMLAs). Logistic regression analyses were performed to screen and identify predictive factors for the novel subtype of LE-PAD and a prediction model was built. We performed a comparative analysis regarding neutrophil levels in different subgroups of patients and an immune cell infiltration analysis to explore the associations between neutrophil levels and LE-PAD. Through hematoxylin and eosin (H&E) staining of lower-extremity arteries, neutrophil infiltration in patients with and without LE-PAD was compared. We found that UMLAs can helped in constructing a prediction model for patients with novel LE-PAD subtypes which enabled risk stratification for patients with LE-PAD using routinely available clinical data to assist clinical decision-making and improve personalized management for patients with LE-PAD. Additionally, the results indicated the critical role of neutrophil infiltration in LE-PAD pathogenesis.
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Affiliation(s)
- Lin Zhang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Yuanliang Ma
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Que Li
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Zhen Long
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Jiangfeng Zhang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Zhanman Zhang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Xiao Qin
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
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Anyaegbunam UA, More P, Fontaine JF, Cate VT, Bauer K, Distler U, Araldi E, Bindila L, Wild P, Andrade-Navarro MA. A Systematic Review of Lipid-Focused Cardiovascular Disease Research: Trends and Opportunities. Curr Issues Mol Biol 2023; 45:9904-9916. [PMID: 38132464 PMCID: PMC10742042 DOI: 10.3390/cimb45120618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Lipids are important modifiers of protein function, particularly as parts of lipoproteins, which transport lipophilic substances and mediate cellular uptake of circulating lipids. As such, lipids are of particular interest as blood biological markers for cardiovascular disease (CVD) as well as for conditions linked to CVD such as atherosclerosis, diabetes mellitus, obesity and dietary states. Notably, lipid research is particularly well developed in the context of CVD because of the relevance and multiple causes and risk factors of CVD. The advent of methods for high-throughput screening of biological molecules has recently resulted in the generation of lipidomic profiles that allow monitoring of lipid compositions in biological samples in an untargeted manner. These and other earlier advances in biomedical research have shaped the knowledge we have about lipids in CVD. To evaluate the knowledge acquired on the multiple biological functions of lipids in CVD and the trends in their research, we collected a dataset of references from the PubMed database of biomedical literature focused on plasma lipids and CVD in human and mouse. Using annotations from these records, we were able to categorize significant associations between lipids and particular types of research approaches, distinguish non-biological lipids used as markers, identify differential research between human and mouse models, and detect the increasingly mechanistic nature of the results in this field. Using known associations between lipids and proteins that metabolize or transport them, we constructed a comprehensive lipid-protein network, which we used to highlight proteins strongly connected to lipids found in the CVD-lipid literature. Our approach points to a series of proteins for which lipid-focused research would bring insights into CVD, including Prostaglandin G/H synthase 2 (PTGS2, a.k.a. COX2) and Acylglycerol kinase (AGK). In this review, we summarize our findings, putting them in a historical perspective of the evolution of lipid research in CVD.
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Affiliation(s)
- Uchenna Alex Anyaegbunam
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
| | - Piyush More
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
- Department of Pharmacology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Jean-Fred Fontaine
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
- Central Institute for Decision Support Systems in Crop Protection (ZEPP), 55545 Bad Kreuznach, Germany
| | - Vincent ten Cate
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), University Medical Center, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Katrin Bauer
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Computational Systems Medicine, Center for Thrombosis and Hemostasis (CTH), 55131 Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Research Centre for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Elisa Araldi
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Computational Systems Medicine, Center for Thrombosis and Hemostasis (CTH), 55131 Mainz, Germany
| | - Laura Bindila
- Institute of Physiological Chemistry, University Medical Center, 55131 Mainz, Germany
| | - Philipp Wild
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), University Medical Center, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
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Khan SA, Ilies MA. The Phospholipase A2 Superfamily: Structure, Isozymes, Catalysis, Physiologic and Pathologic Roles. Int J Mol Sci 2023; 24:ijms24021353. [PMID: 36674864 PMCID: PMC9862071 DOI: 10.3390/ijms24021353] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/23/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
The phospholipase A2 (PLA2) superfamily of phospholipase enzymes hydrolyzes the ester bond at the sn-2 position of the phospholipids, generating a free fatty acid and a lysophospholipid. The PLA2s are amphiphilic in nature and work only at the water/lipid interface, acting on phospholipid assemblies rather than on isolated single phospholipids. The superfamily of PLA2 comprises at least six big families of isoenzymes, based on their structure, location, substrate specificity and physiologic roles. We are reviewing the secreted PLA2 (sPLA2), cytosolic PLA2 (cPLA2), Ca2+-independent PLA2 (iPLA2), lipoprotein-associated PLA2 (LpPLA2), lysosomal PLA2 (LPLA2) and adipose-tissue-specific PLA2 (AdPLA2), focusing on the differences in their structure, mechanism of action, substrate specificity, interfacial kinetics and tissue distribution. The PLA2s play important roles both physiologically and pathologically, with their expression increasing significantly in diseases such as sepsis, inflammation, different cancers, glaucoma, obesity and Alzheimer's disease, which are also detailed in this review.
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Casares-Marfil D, Kerick M, Andrés-León E, Bosch-Nicolau P, Molina I, Martin J, Acosta-Herrera M. GWAS loci associated with Chagas cardiomyopathy influences DNA methylation levels. PLoS Negl Trop Dis 2021; 15:e0009874. [PMID: 34714828 PMCID: PMC8580254 DOI: 10.1371/journal.pntd.0009874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/10/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
A recent genome-wide association study (GWAS) identified a locus in chromosome 11 associated with the chronic cardiac form of Chagas disease. Here we aimed to elucidate the potential functional mechanism underlying this genetic association by analyzing the correlation among single nucleotide polymorphisms (SNPs) and DNA methylation (DNAm) levels as cis methylation quantitative trait loci (cis-mQTL) within this region. A total of 2,611 SNPs were tested against 2,647 DNAm sites, in a subset of 37 chronic Chagas cardiomyopathy patients and 20 asymptomatic individuals from the GWAS. We identified 6,958 significant cis-mQTLs (False Discovery Rate [FDR]<0.05) at 1 Mb each side of the GWAS leading variant, where six of them potentially modulate the expression of the SAC3D1 gene, the reported gene in the previous GWAS. In addition, a total of 268 cis-mQTLs showed differential methylation between chronic Chagas cardiomyopathy patients and asymptomatic individuals. The most significant cis-mQTLs mapped in the gene bodies of POLA2 (FDR = 1.04x10-11), PLAAT3 (FDR = 7.22x10-03), and CCDC88B (FDR = 1.89x10-02) that have been associated with cardiovascular and hematological traits in previous studies. One of the most relevant interactions correlated with hypermethylation of CCDC88B. This gene is involved in the inflammatory response, and its methylation and expression levels have been previously reported in Chagas cardiomyopathy. Our findings support the functional relevance of the previously associated genomic region, highlighting the regulation of novel genes that could play a role in the chronic cardiac form of the disease. Genome-wide association studies (GWAS) have provided extensive information regarding the genetic component of complex traits, including parasitic diseases such as Chagas disease. However, these associations mapped in regulatory regions of the genome and assigning them a functional consequence have been cumbersome. In this study we aimed to evaluate the functional mechanism underlying the previously reported genomic association with chronic Chagas cardiomyopathy, by assessing the correlation between methylation changes and the underlying genetic variations within the region. These methylation quantitative trait loci (mQTLs) may be involved in gene expression regulation. We identified mQTLs in three genes that have been associated with cardiovascular diseases in previous studies. Interestingly, one of these genes was previously identified as differentially methylated and expressed in heart biopsies of chronic Chagas cardiomyopathy patients. Our results suggest novel genes that could play a role in the chronic Chagas cardiomyopathy, evidencing the functional relevance of the previously associated loci.
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Affiliation(s)
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | | | - Pau Bosch-Nicolau
- Unidad de Medicina Tropical y Salud Internacional Hospital Universitari Vall d’Hebron, PROSICS, Barcelona, Spain
| | - Israel Molina
- Unidad de Medicina Tropical y Salud Internacional Hospital Universitari Vall d’Hebron, PROSICS, Barcelona, Spain
| | | | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
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