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Doddi S, Hamoud AR, Eby HM, Zhang X, Imami AS, Shedroff E, Schiefer I, Moreno-Lopez J, Gamm D, Meller J, McCullumsmith RE. Transcriptomic Analysis of Metastatic Uveal Melanoma and Differences in Male and Female Patients. Cancer Genomics Proteomics 2024; 21:350-360. [PMID: 38944422 PMCID: PMC11215432 DOI: 10.21873/cgp.20452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND/AIM Uveal melanoma is an ocular malignancy whose prognosis severely worsens following metastasis. In order to improve the understanding of molecular physiology of metastatic uveal melanoma, we identified genes and pathways implicated in metastatic vs non-metastatic uveal melanoma. PATIENTS AND METHODS A previously published dataset from Gene Expression Omnibus (GEO) was used to identify differentially expressed genes between metastatic and non-metastatic samples as well as to conduct pathway and perturbagen analyses using Gene Set Enrichment Analysis (GSEA), EnrichR, and iLINCS. RESULTS In male metastatic uveal melanoma samples, the gene LOC401052 is significantly down-regulated and FHDC1 is significantly up-regulated compared to non-metastatic male samples. In female samples, no significant differently expressed genes were found. Additionally, we identified many significant up-regulated immune response pathways in male metastatic uveal melanoma, including "T cell activation in immune response". In contrast, many top up-regulated female pathways involve iron metabolism, including "heme biosynthetic process". iLINCS perturbagen analysis identified that both male and female samples have similar discordant activity with growth factor receptors, but only female samples have discordant activity with progesterone receptor agonists. CONCLUSION Our results from analyzing genes, pathways, and perturbagens demonstrate differences in metastatic processes between sexes.
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Affiliation(s)
- Sishir Doddi
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Abdul-Rizaq Hamoud
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Hunter M Eby
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Xiaolu Zhang
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Elizabeth Shedroff
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A
| | - Isaac Schiefer
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, U.S.A
| | - Jose Moreno-Lopez
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, U.S.A
| | - David Gamm
- McPherson Eye Research Institute and Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, U.S.A
| | - Robert E McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, U.S.A.;
- Neurosciences Institute, ProMedica, Toledo, OH, U.S.A
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Njegić A, Laid L, Zi M, Maniati E, Wang J, Chelu A, Wisniewski L, Hunter J, Prehar S, Stafford N, Gilon C, Hoffman A, Weinmüller M, Kessler H, Cartwright EJ, Hodivala-Dilke K. Treatment with αvβ3-integrin-specific 29P attenuates pressure-overload induced cardiac remodelling after transverse aortic constriction in mice. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY PLUS 2024; 8:100069. [PMID: 38933087 PMCID: PMC11196926 DOI: 10.1016/j.jmccpl.2024.100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 06/28/2024]
Abstract
Heart failure remains one of the largest clinical burdens globally, with little to no improvement in the development of disease-eradicating therapeutics. Integrin targeting has been used in the treatment of ocular disease and cancer, but little is known about its utility in the treatment of heart failure. Here we sought to determine whether the second generation orally available, αvβ3-specific RGD-mimetic, 29P , was cardioprotective. Male mice were subjected to transverse aortic constriction (TAC) and treated with 50 μg/kg 29P or volume-matched saline as Vehicle control. At 3 weeks post-TAC, echocardiography showed that 29P treatment significantly restored cardiac function and structure indicating the protective effect of 29P treatment in this model of heart failure. Importantly, 29P treatment improved cardiac function giving improved fractional shortening, ejection fraction, heart weight and lung weight to tibia length fractions, together with partial restoration of Ace and Mme levels, as markers of the TAC insult. At a tissue level, 29P reduced cardiomyocyte hypertrophy and interstitial fibrosis, both of which are major clinical features of heart failure. RNA sequencing identified that, mechanistically, this occurred with concomitant alterations to genes involved molecular pathways associated with these processes such as metabolism, hypertrophy and basement membrane formation. Overall, targeting αvβ3 with 29P provides a novel strategy to attenuate pressure-overload induced cardiac hypertrophy and fibrosis, providing a possible new approach to heart failure treatment.
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Affiliation(s)
- Alexandra Njegić
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Lina Laid
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Min Zi
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Alexandru Chelu
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Laura Wisniewski
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Jenna Hunter
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sukhpal Prehar
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Nicholas Stafford
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Chaim Gilon
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amnon Hoffman
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, P.O. Box 12065, Jerusalem 91120, Israel
| | - Michael Weinmüller
- Institute for Advanced Study, TUM School of Natural Science, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Horst Kessler
- Institute for Advanced Study, TUM School of Natural Science, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Elizabeth J. Cartwright
- Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Kairbaan Hodivala-Dilke
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
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3
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Liu S, Wen H, Li F, Xue X, Sun X, Li F, Hu R, Xi H, Boccellato F, Meyer TF, Mi Y, Zheng P. Revealing the pathogenesis of gastric intestinal metaplasia based on the mucosoid air-liquid interface. J Transl Med 2024; 22:468. [PMID: 38760813 PMCID: PMC11101349 DOI: 10.1186/s12967-024-05276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Gastric intestinal metaplasia (GIM) is an essential precancerous lesion. Although the reversal of GIM is challenging, it potentially brings a state-to-art strategy for gastric cancer therapeutics (GC). The lack of the appropriate in vitro model limits studies of GIM pathogenesis, which is the issue this work aims to address for further studies. METHOD The air-liquid interface (ALI) model was adopted for the long-term culture of GIM cells in the present work. This study conducted Immunofluorescence (IF), quantitative real-time polymerase chain reaction (qRT-PCR), transcriptomic sequencing, and mucoproteomic sequencing (MS) techniques to identify the pathways for differential expressed genes (DEGs) enrichment among different groups, furthermore, to verify novel biomarkers of GIM cells. RESULT Our study suggests that GIM-ALI model is analog to the innate GIM cells, which thus can be used for mucus collection and drug screening. We found genes MUC17, CDA, TRIM15, TBX3, FLVCR2, ONECUT2, ACY3, NMUR2, and MAL2 were highly expressed in GIM cells, while GLDN, SLC5A5, MAL, and MALAT1 showed down-regulated, which can be used as potential biomarkers for GIM cells. In parallel, these genes that highly expressed in GIM samples were mainly involved in cancer-related pathways, such as the MAPK signal pathway and oxidative phosphorylation signal pathway. CONCLUSION The ALI model is validated for the first time for the in vitro study of GIM. GIM-ALI model is a novel in vitro model that can mimic the tissue micro-environment in GIM patients and further provide an avenue for studying the characteristics of GIM mucus. Our study identified new markers of GIM as well as pathways associated with GIM, which provides outstanding insight for exploring GIM pathogenesis and potentially other related conditions.
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Affiliation(s)
- Simeng Liu
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Huijuan Wen
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Fazhan Li
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Fuhao Li
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Ruoyu Hu
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China
| | - Huayuan Xi
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China
| | - Francesco Boccellato
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, 11743, UK
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein - Campus Kiel, Rosalind-Franklin- Straße 12, 24105, Kiel, Germany
| | - Yang Mi
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China.
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China.
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China.
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Alzhrani AA, Rasool M, Karim S, Alhejin A, Haque A, Morsi M, Alama MN, Pushparaj PN. KDM3A knockdown regulates COMP, LOX, COL8A1 and ACOT1 genes in myocardial fibrosis. Bioinformation 2024; 20:305-313. [PMID: 38854759 PMCID: PMC11161882 DOI: 10.6026/973206300200305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 06/11/2024] Open
Abstract
Cardiovascular disease (CVD) is one of the main causes of death in Saudi Arabia. Cardiac remodeling plays a critical role in the pathophysiology of heart failure. Major focus of our study was to identify crucial genes involved in the pathological remodeling of the heart caused by pressure overload. We utilized various in-silico tools to analyze and interpret microarray data obtained from the Gene Expression Omnibus (GEO) database (GSE120739), including GEO2R analysis, Metascape analysis, WebGestalt analysis, and IPA (Ingenuity pathway analysis). Our findings indicate that certain genes, including Cartilage Oligomeric Matrix Protein (COMP), collagen type VIII alpha 1 chain (COL8A1) and Lysyl Oxidase (LOX) under the influence caused by knockdown of KDM3A, were down regulated by the extracellular matrix pathway. Moreover, genes, such as Acyl-CoA Thioesterase 1 (ACOT1) were up regulated by the fatty acid metabolism pathway. Overexpression of lysine-specific demethylase 3A (KDM3A) leads to the up regulation of fibrosis-related genes COMP, COL8A1, and LOX and the down regulation of ACOT1, result in enhanced fibrosis and heart failure. Our results suggest that COMP, COL8A1, LOX, and ACOT1 warrant further investigation in the development of cardiac fibrosis and as potential biomarkers for causing heart failure.
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Affiliation(s)
- Abrar A Alzhrani
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ahmed Alhejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Absarul Haque
- King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed Morsi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohamed Nabil Alama
- Department of Cardiology, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Liu T, Xu C, Guo J, He Z, Zhang Y, Feng Y. Whole Blood Transcriptome Analysis in Patients with Trigeminal Neuralgia: a Prospective Clinical Study. J Mol Neurosci 2024; 74:16. [PMID: 38300339 DOI: 10.1007/s12031-024-02195-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/28/2024] [Indexed: 02/02/2024]
Abstract
Trigeminal neuralgia (TN) brings a huge burden to patients, without long-term effective treatment. This study aimed to explore the differentially expressed genes (DEGs) and related enrichment pathways in patients with TN. This was a study of transcriptome sequencing and bioinformatics analysis of human samples. Whole blood samples were collected from the TN patients and pain-free controls. RNA was extracted to conduct the RNA-sequencing and the subsequent bioinformatics analysis. DEGs between the two groups were derived. Kyoto encyclopedia of genes and genomes (KEGG) and Gene ontology (GO) was used to find the enrichment pathways of DEGs. Protein protein interaction (PPI) network was used to depict the interaction between DEGs and find the most important gene, hub gene. Compared with the control group, there were 117 up-regulated DEGs and 103 down-regulated DEGs in the whole blood of patients in the TN group. Pathway enrichment analysis showed that DEGs were mainly enriched in the neuroimmune and metabolic pathways. The PPI network demonstrated that colony stimulating factor 2 (CSF2) was the most important hub gene in the whole blood of TN patients. This study shows the expression of the transcriptome in the whole blood samples of TN patients. The neuroimmune responses and key hub gene CSF2 in the whole blood cells play a vital role in the occurrence of TN. Our research provides a theoretical basis for the diagnosis and treatments of TN. This study was registered at clinicaltrials.gov in June 2021 (No. NCT04923399).
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Affiliation(s)
- Tianyu Liu
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Chao Xu
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Guo
- Shanghai Minhang Center for Disease Control and Prevention, Shanghai, China
| | - Zile He
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Yunpeng Zhang
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Yi Feng
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Xueyuan road 38, Beijing, 100191, China.
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Transcriptomic Profile of Genes Regulating the Structural Organization of Porcine Atrial Cardiomyocytes during Primary In Vitro Culture. Genes (Basel) 2022; 13:genes13071205. [PMID: 35885988 PMCID: PMC9319992 DOI: 10.3390/genes13071205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Numerous cardiovascular diseases (CVD) eventually lead to severe myocardial dysfunction, which is the most common cause of death worldwide. A better understanding of underlying molecular mechanisms of cardiovascular pathologies seems to be crucial to develop effective therapeutic options. Therefore, a worthwhile endeavor is a detailed molecular characterization of cells extracted from the myocardium. A transcriptomic profile of atrial cardiomyocytes during long-term primary cell culture revealed the expression patterns depending on the duration of the culture and the heart segment of origin (right atrial appendage and right atrium). Differentially expressed genes (DEGs) were classified as involved in ontological groups such as: “cellular component assembly”, “cellular component organization”, “cellular component biogenesis”, and “cytoskeleton organization”. Transcriptomic profiling allowed us to indicate the increased expression of COL5A2, COL8A1, and COL12A1, encoding different collagen subunits, pivotal in cardiac extracellular matrix (ECM) structure. Conversely, genes important for cellular architecture, such as ABLIM1, TMOD1, XIRP1, and PHACTR1, were downregulated during in vitro culture. The culture conditions may create a favorable environment for reconstruction of the ECM structures, whereas they may be suboptimal for expression of some pivotal transcripts responsible for the formation of intracellular structures.
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Song H, Chen S, Zhang T, Huang X, Zhang Q, Li C, Chen C, Chen S, Liu D, Wang J, Tu Y, Wu Y, Liu Y. Integrated Strategies of Diverse Feature Selection Methods Identify Aging-Based Reliable Gene Signatures for Ischemic Cardiomyopathy. Front Mol Biosci 2022; 9:805235. [PMID: 35300115 PMCID: PMC8921505 DOI: 10.3389/fmolb.2022.805235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
Objective: Ischemic cardiomyopathy (ICM) is a major cardiovascular state associated with prominently increased morbidity and mortality. Our purpose was to detect reliable gene signatures for ICM through integrated feature selection strategies.Methods: Transcriptome profiles of ICM were curated from the GEO project. Classification models, including least absolute shrinkage and selection operator (LASSO), support vector machine (SVM), and random forest, were adopted for identifying candidate ICM-specific genes for ICM. Immune cell infiltrates were estimated using the CIBERSORT method. Expressions of candidate genes were verified in ICM and healthy myocardial tissues via Western blotting. JC-1 staining, flow cytometry, and TUNEL staining were presented in hypoxia/reoxygenation (H/R)-stimulated H9C2 cells with TRMT5 deficiency.Results: Following the integration of three feature selection methods, we identified seven candidate ICM-specific genes including ASPN, TRMT5, LUM, FCN3, CNN1, PCNT, and HOPX. ROC curves confirmed the excellent diagnostic efficacy of this combination of previous candidate genes in ICM. Most of them presented prominent interactions with immune cell infiltrates. Their deregulations were confirmed in ICM than healthy myocardial tissues. TRMT5 expressions were remarkedly upregulated in H/R-stimulated H9C2 cells. TRMT5 deficiency enhanced mitochondrial membrane potential and reduced apoptosis in H/R-exposed H9C2 cells.Conclusion: Collectively, our findings identified reliable gene signatures through combination strategies of diverse feature selection methods, which facilitated the early detection of ICM and revealed the underlying mechanisms.
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Affiliation(s)
- Huafeng Song
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shaoze Chen
- Department of Cardiology, Huanggang Central Hospital, Huanggang, China
| | - Tingting Zhang
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaofei Huang
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qiyu Zhang
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Cuizhi Li
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chunlin Chen
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shaoxian Chen
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, School of Medicine, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, South China University of Technology, Guangzhou, China
| | - Dehui Liu
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiawen Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Jiawen Wang, ; Yingfeng Tu, ; Yueheng Wu, ; Youbin Liu,
| | - Yingfeng Tu
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Jiawen Wang, ; Yingfeng Tu, ; Yueheng Wu, ; Youbin Liu,
| | - Yueheng Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, School of Medicine, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, South China University of Technology, Guangzhou, China
- *Correspondence: Jiawen Wang, ; Yingfeng Tu, ; Yueheng Wu, ; Youbin Liu,
| | - Youbin Liu
- Department of Cardiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jiawen Wang, ; Yingfeng Tu, ; Yueheng Wu, ; Youbin Liu,
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8
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Guo Y, Ning B, Zhang Q, Ma J, Zhao L, Lu Q, Zhang D. Identification of Hub Diagnostic Biomarkers and Candidate Therapeutic Drugs in Heart Failure. Int J Gen Med 2022; 15:623-635. [PMID: 35058712 PMCID: PMC8765546 DOI: 10.2147/ijgm.s349235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/31/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose The objective of this study was to identify the potential regulatory mechanisms, diagnostic biomarkers, and therapeutic drugs for heart failure (HF). Methods Differentially expressed genes (DEGs) between HF and non-failing donors were screened from the GSE57345, GSE5406, and GSE3586 datasets. Database for Annotation Visualization and Integrated Discovery and Metascape were used for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses respectively. The GSE57345 dataset was used for weighted gene co-expression network analysis (WGCNA). The intersecting hub genes from the DEGs and WGCNA were identified and verified with the GSE5406 and GSE3586 datasets. The diagnostic value of the hub genes was calculated through receiver operating characteristic analysis and net reclassification index (NRI). Gene set enrichment analysis (GSEA) was used to filter out the signaling pathways associated with the hub genes. SYBYL 2.1 was used for molecular docking of hub targets and potential HF drugs obtained from the connection map. Results Functional annotation of the DEGs showed enrichment of negative regulation of angiogenesis, endoplasmic reticulum stress response, and heart development. PTN, LUM, ISLR, and ASPN were identified as the hub genes of HF. GSEA showed that the key genes were related to the transforming growth factor-β (TGF-β) and Wnt signaling pathways. Sirolimus, LY-294002, and wortmannin have been confirmed as potential drugs for HF. Conclusion We identified new hub genes and candidate therapeutic drugs for HF, which are potential diagnostic, therapeutic and prognostic targets and warrant further investigation.
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Affiliation(s)
- Yang Guo
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Qinghai-Utah Joint Research Key Lab for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
| | - Bobin Ning
- Department of Medicine, The General Hospital of the People's Liberation Army, Beijing, 100038, People's Republic of China
| | - Qunhui Zhang
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Qinghai-Utah Joint Research Key Lab for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
| | - Jing Ma
- Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
| | - Linlin Zhao
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Qinghai-Utah Joint Research Key Lab for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
| | - QiQin Lu
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Qinghai-Utah Joint Research Key Lab for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
| | - Dejun Zhang
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, People's Republic of China.,Department of Eco-Environmental Engineering, Qinghai University, Xining, 810016, People's Republic of China
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9
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Liu B, Gou W, Feng H. Pathological investigations and correlation research of microfibrillar-associated protein 4 and tropoelastin in oral submucous fibrosis. BMC Oral Health 2021; 21:588. [PMID: 34798886 PMCID: PMC8603475 DOI: 10.1186/s12903-021-01962-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Background Oral submucous fibrosis (OSF), distinguished by abnormal collagen deposition, is a potentially malignant disorder with 4.2% (95% CI 2.7–5.6%) of malignant transformation and rising global prevalence. However, the precise pathogenesis and effective treatment remain elusive and controversial despite the abundance of literature on this topic. Therefore, it is crucial to explore the clinicopathological characteristics and potential markers for the diagnosis and prognosis of OSF. The objective of this study was to evaluate the influence and correlation of Microfibrillar-associated protein 4 (MFAP4) and tropoelastin (TE) in the development of OSF patients. Material and methods Clinicopathological factors, hematoxylin–eosin (HE) and Masson trichome staining, immunohistochemical characteristics and the correlation between MFAP4 and TE were recorded and compared among different stages of OSF progression among cases (n = 60) and controls (n = 10). Student's t test, ANOVA analysis, and the chi-square test were performed to compare the categorical variables for clinicopathological characteristics and the expression level of MFAP4 and TE between the fibrotic and normal tissues. Correlation analysis of MFAP4 and TE was performed using Pearson's correlation test and linear regression. Results MFAP4 and TE proteins are upregulated and increased gradually in patients with varying stages of OSF, relative to the control group. Furthermore, statistical analyses revealed that the expression level of MFAP4 was positively associated with TE, with a Pearson correlation coefficient of 0.3781 (p = 0.0048). Clinically, we found that OSF affected more males than females, with a ratio of 29:1. The age range was 16–60 years, and the mean age was 36.25 ± 10.25 years. In patients younger than 40 years, the positive expression rate of MFAP4 and TE was higher than in those over 40 years. All OSF cases had chewed areca nut, with 51.67% smoking tobacco. Conclusions Our study elucidates that the accumulation of MFAP4 and TE proteins may play a vital role in the occurrence and development of OSF and may be promising candidate moleculars for prevention, diagnosis, and treatment strategies for OSF in the future.
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Affiliation(s)
- Binjie Liu
- Department of Oral Medicine, Xiangya Stomalogical Hospital, Central South University, Changsha, China
| | - Wenqun Gou
- Department of Oral Medicine, Xiangya Stomalogical Hospital, Central South University, Changsha, China.,Changsha Stomatological Hospital, Changsha, China
| | - Hui Feng
- Department of Oral Medicine, Xiangya Stomalogical Hospital, Central South University, Changsha, China.
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10
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Yang R, Ma M, Yu S, Li X, Zhang J, Wu S. High Expression of PAMR1 Predicts Favorable Prognosis and Inhibits Proliferation, Invasion, and Migration in Cervical Cancer. Front Oncol 2021; 11:742017. [PMID: 34671559 PMCID: PMC8521121 DOI: 10.3389/fonc.2021.742017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Peptidase domain containing associated with muscle regeneration 1 (PAMR1) is frequently lost in breast cancer samples and is considered as a tumor suppressor. The roles and mechanisms of PAMR1 in other types of cancers are still unclear. In our present study, we identified PAMR1 as an invasion-related regulator in cervical cancer. Public database and immunohistochemical (IHC) analysis showed that the expression level of PAMR1 in cervical cancer tissues was lower than that in normal cervix tissues and was negatively related to clinicopathologic features. The high expression of PAMR1 also predicted a better prognosis of cervical cancer patients. CCK8, Transwell, and wound-healing assays demonstrated that knockdown of PAMR1 facilitated the proliferation, migration, and invasion of cervical cancer cells. Additionally, gene set enrichment analysis (GSEA) showed a variety of cancer-related pathways potentially activated or suppressed by PAMR1. Moreover, we verified that PAMR1 inhibited MYC target and mTORC1 signaling pathways. In conclusion, our study revealed the suppressor role of PAMR1 in cervical cancer, providing a new insight into the molecular mechanism of cervical cancer progression.
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Affiliation(s)
- Rui Yang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingjun Ma
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sihui Yu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiawen Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Reproductive Medicine Center, Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sufang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Li Q, Lai Y, Gao X, Li X, Deng CY, Guo H, Zhao J, Yang H, Xu Y, Wu S, Xue Y, Rao F. Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation. PeerJ 2021; 9:e11488. [PMID: 34141473 PMCID: PMC8179226 DOI: 10.7717/peerj.11488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/27/2021] [Indexed: 12/01/2022] Open
Abstract
Atrial fibrillation is the most common form of cardiac arrhythmia. Atrial fibrosis is a significant feature of atrial fibrillation though its mechanism is not well understood. We searched the Gene Expression Omnibus database to compare mRNA expression patterns between atrial fibrillation and sinus rhythm samples; one hundred and forty eight differentially expressed genes were identified. Most of these genes were significantly enriched in the extracellular matrix organization process and collagen-activated tyrosine kinase receptor signaling pathway. To screen hub genes involved in atrial fibrosis, we constructed a protein-protein interaction network and found that three hub genes (SERPINE1/plasminogen activator inhibitor-1/PAI-1, TIMP Metallopeptidase Inhibitor 3/TIMP3 and decorin/DCN) play vital roles in atrial fibrosis, especially plasminogen activator inhibitor-1. Elevated plasminogen activator inhibitor-1 expression was positively correlated with the p53 signaling pathway. Plasminogen activator inhibitor-1 and p53 protein expression levels were verified in patients with sinus rhythm and atrial fibrillation by Western blot analysis. Compared with the sinus rhythm controls, p53 and plasminogen activator inhibitor-1 protein expressions were upregulated in the atrial tissues of patients with atrial fibrillation. p53 was also found to regulate plasminogen activator inhibitor-1 based on the results of cellular and molecular experiments. Thus, the p53/plasminogen activator inhibitor-1 signaling axis may participate in the pathophysiological processes of atrial fibrillation, and plasminogen activator inhibitor-1 may serve as a new therapeutic biomarker in atrial fibrillation.
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Affiliation(s)
- Qiaoqiao Li
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Yingyu Lai
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xiaoyan Gao
- School of Medicine, South China University of Technology, Guangzhou, China.,Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xin Li
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Chun-Yu Deng
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Huiming Guo
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junfei Zhao
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hui Yang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Yuwen Xu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Shulin Wu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Yumei Xue
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Fang Rao
- School of Medicine, South China University of Technology, Guangzhou, China.,Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Pharmacology, Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
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12
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Zhu Y, Wang Q, Lin H, Chen K, Zheng C, Chen L, Ma S, Liao W, Bin J, Liao Y. Characterizing a long-term chronic heart failure model by transcriptomic alterations and monitoring of cardiac remodeling. Aging (Albany NY) 2021; 13:13585-13614. [PMID: 33891565 PMCID: PMC8202904 DOI: 10.18632/aging.202879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
The long-term characteristics of transcriptomic alterations and cardiac remodeling in chronic heart failure (CHF) induced by myocardial infarction (MI) in mice are not well elucidated. This study aimed to reveal the dynamic changes in the transcriptome and cardiac remodeling in post-MI mice over a long time period. Monitoring C57BL/6 mice with MI for 8 months showed that approximately 44% of mice died of cardiac rupture in the first 2 weeks and others survived to 8 months with left ventricular (LV) aneurysm. The transcriptomic profiling analysis of cardiac tissues showed that the Integrin and WNT pathways were activated at 8 months after MI while the metabolism-related pathways were inversely inhibited. Subsequent differential analysis at 1 and 8 months post-MI revealed significant enrichments in biological processes, including consistent regulation of metabolism-related pathways. Moreover, echocardiographic monitoring showed a progressive increase in LV dimensions and a decrease in the LV fractional shortening during the first 4 weeks, and these parameters progressed at a lower rate till 8 months. A similar trend was found in the invasive LV hemodynamics, cardiac morphological and histological analyses. These results suggested that mouse MI model is ideal for long-term studies, and transcriptomic findings may provide new CHF therapeutic targets.
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Affiliation(s)
- Yingqi Zhu
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qiancheng Wang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hairuo Lin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kaitong Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Cankun Zheng
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Lin Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Siyuan Ma
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Lab of Shock and Microcirculation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
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13
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Zhu X, Zhang F, Lian S, Wang Y, Hu N, Chen X, Dai X, Hu X, Wang S, Bao Z. IAPs Gene Expansion in the Scallop Patinopecten yessoensis and Their Expression Profiles After Exposure to the Toxic Dinoflagellate. Front Physiol 2021; 12:633301. [PMID: 33613325 PMCID: PMC7893105 DOI: 10.3389/fphys.2021.633301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/15/2021] [Indexed: 01/17/2023] Open
Abstract
Inhibitors of apoptosis proteins (IAPs) are conserved regulators involved in cell cycle, cell migration, cell death, immunity and inflammation, should be due to the fact that they can assist with the ability to cope with different kinds of extrinsic or intrinsic stresses. Bivalve molluscs are well adapted to highly complex marine environments. As free-living filter feeders that may take toxic dinoflagellates as food, bivalves can accumulate and put up with significant levels of paralytic shellfish toxins (PSTs). PSTs absorption and accumulation could have a deleterious effect on bivalves, causing negative impact on their feeding and digestion capabilities. In the present study, we analyzed IAP genes (PyIAPs) in Yesso scallop (Patinopecten yessoensis), a major fishery and aquaculture species in China. Forty-seven PyIAPs from five sub-families were identified, and almost half of the PyIAP genes were localized in clusters on two chromosomes. Several sites under positive selection was revealed in the significantly expanded sub-families BIRC4 and BIRC5. After exposure to PST-producing dinoflagellates, Alexandrium catenella, fourteen PyIAPs showed significant responses in hepatopancreas and kidney, and more than eighty-five percent of them were from the expanded sub-families BIRC4 and BIRC5. The regulation pattern of PyIAPs was similar between the two tissues, with more than half exhibited expression suppression within three days after exposure. In contrast to hepatopancreas, more acute changes of PyIAPs expression could be detected in kidney, suggesting the possible involvement of these PyIAPs in tissue-specific PST tolerance. These findings also imply the adaptive expansion of bivalve IAP genes in response to algae derived biotoxins.
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Affiliation(s)
- Xiaomei Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Fengmei Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yinghui Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Naina Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiaomei Chen
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Tomin T, Schittmayer M, Sedej S, Bugger H, Gollmer J, Honeder S, Darnhofer B, Liesinger L, Zuckermann A, Rainer PP, Birner-Gruenberger R. Mass Spectrometry-Based Redox and Protein Profiling of Failing Human Hearts. Int J Mol Sci 2021; 22:ijms22041787. [PMID: 33670142 PMCID: PMC7916846 DOI: 10.3390/ijms22041787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of the antioxidative defense, dysregulation of redox signaling, and protein damage. In order to precisely dissect the changes of the myocardial redox state correlated with oxidative stress and heart failure, we subjected left-ventricular tissue specimens collected from control or failing human hearts to comprehensive mass spectrometry-based redox and quantitative proteomics, as well as glutathione status analyses. As a result, we report that failing hearts have lower glutathione to glutathione disulfide ratios and increased oxidation of a number of different proteins, including constituents of the contractile machinery as well as glycolytic enzymes. Furthermore, quantitative proteomics of failing hearts revealed a higher abundance of proteins responsible for extracellular matrix remodeling and reduced abundance of several ion transporters, corroborating contractile impairment. Similar effects were recapitulated by an in vitro cell culture model under a controlled oxygen atmosphere. Together, this study provides to our knowledge the most comprehensive report integrating analyses of protein abundance and global and peptide-level redox state in end-stage failing human hearts as well as oxygen-dependent redox and global proteome profiles of cultured human cardiomyocytes.
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Affiliation(s)
- Tamara Tomin
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Matthias Schittmayer
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Simon Sedej
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Heiko Bugger
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Johannes Gollmer
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Sophie Honeder
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Andreas Zuckermann
- Cardiac Transplantation, Department of Cardiac Surgery, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria;
| | - Peter P. Rainer
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Ruth Birner-Gruenberger
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
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15
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Dorn LE, Lawrence W, Petrosino JM, Xu X, Hund TJ, Whitson BA, Stratton MS, Janssen PML, Mohler PJ, Schlosser A, Sorensen GL, Accornero F. Microfibrillar-Associated Protein 4 Regulates Stress-Induced Cardiac Remodeling. Circ Res 2021; 128:723-737. [PMID: 33530700 DOI: 10.1161/circresaha.120.317146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Lisa E Dorn
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
| | - William Lawrence
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
| | - Jennifer M Petrosino
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
| | - Xianyao Xu
- Biomedical Engineering, The Ohio State University, Columbus (X.X., T.J.H.)
| | - Thomas J Hund
- Biomedical Engineering, The Ohio State University, Columbus (X.X., T.J.H.)
| | - Bryan A Whitson
- Bob and Corrine Frick Center for Heart Failure and Arrhythmia (B.A.W., P.J.M.), The Ohio State University Wexner Medical Center, Columbus.,Dorothy M. Davis Heart and Lung Research Institute and Surgery (B.A.W.), The Ohio State University Wexner Medical Center, Columbus
| | - Matthew S Stratton
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
| | - Paul M L Janssen
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
| | - Peter J Mohler
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus.,Bob and Corrine Frick Center for Heart Failure and Arrhythmia (B.A.W., P.J.M.), The Ohio State University Wexner Medical Center, Columbus
| | - Anders Schlosser
- Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense (A.S., G.L.S.)
| | - Grith L Sorensen
- Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense (A.S., G.L.S.)
| | - Federica Accornero
- Physiology and Cell Biology (L.E.D., W.L., J.M.P., M.S.S., P.M.L.J., P.J.M., F.A.), The Ohio State University Wexner Medical Center, Columbus
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16
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Wang HB, Yang J, Shuai W, Yang J, Liu LB, Xu M, Tang QZ. Deletion of Microfibrillar-Associated Protein 4 Attenuates Left Ventricular Remodeling and Dysfunction in Heart Failure. J Am Heart Assoc 2020; 9:e015307. [PMID: 32856514 PMCID: PMC7660778 DOI: 10.1161/jaha.119.015307] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Cardiac remodeling predisposes individuals to heart failure if the burden is not solved, and heart failure is a growing cause of morbidity and mortality worldwide. The cardiac extracellular matrix not only provides structural support, but also is a core aspect of the myocardial response to various biomechanical stresses and heart failure. MFAP4 (microfibrillar‐associated protein 4) is an integrin ligand located in the extracellular matrix, whose biological functions in the heart remain poorly understood. In the current study we aimed to test the role of MFAP4 in cardiac remodeling. Methods and Results MFAP4‐deficient (MFAP4−/−) and wild‐type mice were subjected to aortic banding surgery and isoproterenol to establish models of cardiac remodeling. We also evaluated the functional effects of MFAP4 on cardiac hypertrophy, fibrosis, and cardiac electrical remodeling. The expression of MFAP4 was increased in the animal cardiac remodeling models induced by pressure overload and isoproterenol. After challenge of 8 weeks of aortic banding or 2 weeks of intraperitoneal isoproterenol, MFAP4−/− mice exhibited lower levels of cardiac fibrosis and fewer ventricular arrhythmias than wild‐type mice. However, there was no significant effect on cardiomyocyte hypertrophy. In addition, there was no significant difference in cardiac fibrosis severity, hypertrophy, or ventricular arrhythmia incidence between wild‐type‐sham and knockout‐sham mice. Conclusions These findings are the first to demonstrate that MFAP4 deficiency inhibits cardiac fibrosis and ventricular arrhythmias after challenge with 8 weeks of aortic banding or 2 weeks of intraperitoneal isoproterenol but does not significantly affect the hypertrophy response. In addition, MFAP4 deficiency had no significant effect on cardiac fibrosis, hypertrophy, or ventricular arrhythmia in the sham group in this study.
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Affiliation(s)
- Hui-bo Wang
- Department of CardiologyRenmin Hospital of Wuhan UniversityWuhanChina
- Hubei Key Laboratory of Metabolic and Chronic DiseasesWuhanChina
- Department of CardiologyThree Gorges University People’s HospitalThe First People’s Hospital of YichangYichangChina
| | - Jian Yang
- Department of CardiologyThree Gorges University People’s HospitalThe First People’s Hospital of YichangYichangChina
| | - Wei Shuai
- Department of CardiologyRenmin Hospital of Wuhan UniversityWuhanChina
- Hubei Key Laboratory of Metabolic and Chronic DiseasesWuhanChina
| | - Jun Yang
- Department of CardiologyThe First College of Clinical Medical ScienceChina Three Gorges UniversityYichangChina
- Institute of Cardiovascular DiseasesChina Three Gorges UniversityYichangChina
| | - Li-bo Liu
- Department of CardiologyRenmin Hospital of Wuhan UniversityWuhanChina
- Hubei Key Laboratory of Metabolic and Chronic DiseasesWuhanChina
| | - Man Xu
- Department of CardiologyRenmin Hospital of Wuhan UniversityWuhanChina
- Hubei Key Laboratory of Metabolic and Chronic DiseasesWuhanChina
| | - Qi-zhu Tang
- Department of CardiologyRenmin Hospital of Wuhan UniversityWuhanChina
- Hubei Key Laboratory of Metabolic and Chronic DiseasesWuhanChina
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Fajarda O, Duarte-Pereira S, Silva RM, Oliveira JL. Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Min 2020; 13:8. [PMID: 32670412 PMCID: PMC7346458 DOI: 10.1186/s13040-020-00217-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature deaths. A large amount of microarray data is available in public repositories and can be used to identify differentially expressed genes. However, most of the microarray datasets are composed of a reduced number of samples and to obtain more reliable results, several datasets have to be merged, which is a challenging task. The identification of differentially expressed genes is commonly done using statistical methods. Nonetheless, these methods are based on the definition of an arbitrary threshold to select the differentially expressed genes and there is no consensus on the values that should be used. RESULTS Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features. Subsequently, the adjusted p-value and fold change were determined and by combining a set of adjusted p-values cutoffs with a list of different fold change thresholds, 12 sets of differentially expressed genes were obtained. To select the set of differentially expressed genes that has the best accuracy in classifying samples from patients with heart diseases and samples from patients with no heart condition, the random forest algorithm was used. A set of 62 differentially expressed genes having a classification accuracy of approximately 95% was identified. CONCLUSIONS We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart. The approach used in this study is suitable for the identification of gene expression signatures, and can be extended to different diseases.
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Affiliation(s)
- Olga Fajarda
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Sara Duarte-Pereira
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Raquel M. Silva
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
- Current Address: Universidade Católica Portuguesa, Faculdade de Medicina Dentária, CIIS-Centro de Investigação Interdisciplinar em Saúde, Campus de Viseu, Viseu, 3504-505 Portugal
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Kara SP, Özkan G, Gür DÖ, Emeksiz GK, Yılmaz A, Bayrakçı N, Güzel S. Relationship between Microfibrillar-Associated Protein 4 Levels and Subclinical Myocardial Damage in Chronic Kidney Disease. Cardiorenal Med 2020; 10:257-265. [PMID: 32268335 DOI: 10.1159/000506827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/22/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD) is a widespread health problem, in which mortality is most frequently due to cardiovascular diseases. Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix protein. MFAP4 is involved in several biological processes, particularly the maintenance of vascular integrity and extracellular matrix remodeling. Our review of the literature revealed no data concerning MFAP4 levels in CKD and its relationship with myocardial functions. OBJECTIVE The purpose of this study was therefore to investigate MFAP4 levels in CKD, parameters affecting these, and the relationship with myocardial functions. MATERIALS AND METHODS Seventy-nine CKD patients and 30 healthy controls were included in the study. Routine biochemical tests and echocardiography were performed once demographic data had been recorded. Blood specimens were collected for MFAP4 analysis, and the results were subjected to statistical analysis. RESULTS MFAP4 levels were significantly higher in the patient group than in the control group (p< 0.001). Doppler parameters revealed more frequent LV diastolic impairment in the patient group. Tissue Doppler systolic velocity and global longitudinal strain were significantly impaired, revealing the subclinical LV systolic dysfunction in CKD patients. MFAP4 elevation in the patient group was positively correlated with aortic root (AR), global circumferential strain (GCS), and GCS rate. CONCLUSION Our results showed MFAP4 elevation in CKD for the first time in the literature, and that this elevation may be related to GCS and AR dilation. We think that, once supported by further studies, MFAP4 may constitute a marker in the evaluation of myocardial functions in CKD.
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Affiliation(s)
- Sonat Pınar Kara
- Department of Internal Medicine, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Gülsüm Özkan
- Department of Nephrology, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey,
| | - Demet Özkaramanlı Gür
- Department of Cardiology, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Gaye Kübra Emeksiz
- Department of Internal Medicine, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Ahsen Yılmaz
- Department of Biochemistry, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Nergiz Bayrakçı
- Department of Nephrology, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Savaş Güzel
- Department of Biochemistry, Tekirdağ Namık Kemal University School of Medicine, Tekirdağ, Turkey
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