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Liu Q, Lin Z, Yue M, Wu J, Li L, Huang D, Fang Y, Zhang X, Hao T. Identification and validation of ferroptosis related markers in erythrocyte differentiation of umbilical cord blood-derived CD34 + cell by bioinformatic analysis. Front Genet 2024; 15:1365232. [PMID: 39139819 PMCID: PMC11319168 DOI: 10.3389/fgene.2024.1365232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Ferroptosis has been observed to play an important role during erythrocyte differentiation (ED). However, the biological gene markers and ferroptosis mechanisms in ED remain unknown. We downloaded the datasets of ED in human umbilical cord blood-derived CD34+ cells from the Gene Expression Omnibus database. Using median differentiation time, the sample was categorized into long and short groups. The differentially expressed ferroptosis-related genes (DE-FRGs) were screened using differential expression analysis. The enrichment analyses and a protein-protein interaction (PPI) network were conducted. To predict the ED stage, a logistic regression model was constructed using the least absolute shrinkage and selection operator (LASSO). Overall, 22 DE-FRGs were identified. Ferroptosis-related pathways were enriched using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Gene Set Enrichment Analysis and Gene Set Variation Analysis revealed the primary involvement of DE-FRGs in JAK-STAT, MAPK, PI3K-AKT-mTORC1, WNT, and NOTCH signaling pathways. Ten-hub DE-FRGs were obtained using PPI analysis. Furthermore, we constructed mRNA-microRNA (miRNA) and mRNA-transcription factor networks. Immune cell infiltration levels differed significantly during ED. LASSO regression analysis established a signature using six DE-FRGs (ATF3, CDH2, CHAC1, DDR2, DPP4, and GDF15) related to the ED stage. Bioinformatic analyses identified ferroptosis-associated genes during ED, which were further validated. Overall, we identified ferroptosis-related genes to predict their correlations in ED. Exploring the underlying mechanisms of ferroptosis may help us better understand pathophysiological changes in ED and provide new evidence for clinical transformation.
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Affiliation(s)
- Qian Liu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Ze Lin
- Shantou University Medical College, Shantou, Guangdong, China
| | - Minghui Yue
- Shantou University Medical College, Shantou, Guangdong, China
| | - Jianbo Wu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Lei Li
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Daqi Huang
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Yipeng Fang
- Department of Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Zhang
- Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Molecular Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Tao Hao
- Department of Colorectal Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, China
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Moresi V, Adamo S, Berghella L. The JAK/STAT Pathway in Skeletal Muscle Pathophysiology. Front Physiol 2019; 10:500. [PMID: 31114509 PMCID: PMC6502894 DOI: 10.3389/fphys.2019.00500] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 04/08/2019] [Indexed: 12/29/2022] Open
Abstract
The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is a key intracellular mediator of a variety of metabolically relevant hormones and cytokines, including the interleukin-6 (IL-6) family of cytokines. The JAK/STAT pathway transmits extracellular signals to the nucleus, leading to the transcription of genes involved in multiple biological activities. The JAK/STAT pathway has been reported to be required for the homeostasis of different tissues and organs. Indeed, when deregulated, it promotes the initiation and progression of pathological conditions, including cancer, obesity, diabetes, and other metabolic diseases. In skeletal muscle, activation of the JAK/STAT pathway by the IL-6 cytokines accounts for opposite effects: on the one hand, it promotes muscle hypertrophy, by increasing the proliferation of satellite cells; on the other hand, it contributes to muscle wasting. The expression of IL-6 and of key members of the JAK/STAT pathway is regulated at the epigenetic level through histone methylation and histone acetylation mechanisms. Thus, manipulation of the JAK/STAT signaling pathway by specific inhibitors and/or drugs that modulate epigenetics is a promising therapeutic intervention for the treatment of numerous diseases. We focus this review on the JAK/STAT pathway functions in striated muscle pathophysiology and the potential role of IL-6 as an effector of the cross talk between skeletal muscle and other organs.
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Affiliation(s)
- Viviana Moresi
- Unit of Histology and Medical Embryology, DAHFMO, University La Sapienza, Rome, Italy.,Interuniversity Institute of Myology, Rome, Italy
| | - Sergio Adamo
- Unit of Histology and Medical Embryology, DAHFMO, University La Sapienza, Rome, Italy.,Interuniversity Institute of Myology, Rome, Italy
| | - Libera Berghella
- Unit of Histology and Medical Embryology, DAHFMO, University La Sapienza, Rome, Italy.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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Wang X, Kadarmideen HN. An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits. Front Genet 2019; 10:405. [PMID: 31114612 PMCID: PMC6502962 DOI: 10.3389/fgene.2019.00405] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research. Testis is the main organ for reproduction and boar taint in pigs; however, there have been no studies to-date on adult pig testis epigenome. The main objective of this study was to establish a genome-wide DNA methylation map of pig testis that would help identify candidate epigenetic biomarkers and methylated genes for complex traits such as male reproduction, fertility or boar taint. Reduced Representation Bisulfite Sequencing (RRBS) was used to study methylation levels of cytosine in nine pig testis samples. The results showed that genome-wide methylation status of nine samples overlapped greatly and their variation among pigs were low. The methylation levels of promoter, exon, intron, cytosine and guanine dinucleotide (CpG) islands and CpG island shores regions were 0.15, 0.47, 0.55, 0.39, and 0.53, respectively. Cytosines binding to CpG islands showed different methylation levels between exon and intron regions. All methylation levels of CpG islands were lower than CpG island shores in different genic features. The distribution of 12,738 differentially methylated cytosines (DMCs) within CpG islands, CpG island shores and other regions was 36.86, 21.65, and 41.49%, respectively, and was 0.33, 1.71, 5.95, and 92.01% in promoter, exon, intron and intergenic regions, respectively. Methylation levels of DMCs in promoter, exon and intron regions were significantly different between CpG islands and CpG island shores (P < 0.05). A total of 898 genes with 2089 DMCs were enriched in 112 Gene Ontology (GO) terms. Fifteen methylated genes from our study were associated with fertility or boar taint traits. Our analysis revealed the methylation patterns in different genic features and CpG island regions of testis in pigs, and summarized several candidate genes associated with DMCs and the involved GO terms. These findings are helpful to understand the relationship between DNA methylation and genic CpG islands, to provide candidate epigenetic regions or biomarkers for pig production and welfare and for translational epigenomic studies that use pigs as an animal model for human research.
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Affiliation(s)
- Xiao Wang
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
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Huang LH, Kuo HC, Pan CT, Lin YS, Huang YH, Li SC. Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration. Clin Epigenetics 2018; 10:135. [PMID: 30382880 PMCID: PMC6211403 DOI: 10.1186/s13148-018-0557-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Kawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In addition, globally, to what extent DNA methylation affects gene expression and how it contributes to the pathogenesis of KD are not yet well understood. Methods To address these important biological questions, we enrolled subjects, collected DNA and RNA samples from the subjects’ total white blood cells, and performed DNA methylation (M450K) and gene expression (HTA 2.0) microarray assays. Results By analyzing the variation ratios of CpG beta values (methylation percentage) and gene expression intensities, we first concluded that the CpG markers close (− 1500 bp to + 500 bp) to the transcription start sites had higher variation ratios, reflecting significant regulation capacities. Next, we observed that, globally speaking, gene expression was modestly negatively correlated (correlation rho ≈ − 0.2) with the DNA methylation status of both upstream and downstream CpG markers in the promoter region. Third, we found that specific CpG markers were hypo-methylated in disease samples compared with healthy samples and hyper-methylated in convalescent samples compared with disease samples, promoting and repressing S100A genes’ expressions, respectively. Finally, using an in vitro cell model, we demonstrated that S100A family proteins enhanced leukocyte transendothelial migration in KD. Conclusions This is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD. Electronic supplementary material The online version of this article (10.1186/s13148-018-0557-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ying-Hsien Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan.
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Poz D, De Falco E, Pisano C, Madonna R, Ferdinandy P, Balistreri CR. Diagnostic and Prognostic Relevance of Red Blood Cell Distribution Width for Vascular Aging and Cardiovascular Diseases. Rejuvenation Res 2018; 22:146-162. [PMID: 30132390 DOI: 10.1089/rej.2018.2094] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Evidence suggests association of red blood cell distribution width (RDW) with cardiovascular diseases (CVDs). On the contrary, we underline that the sole RDW values cannot represent a valid CVD biomarker. High RDW values are expression of biological effects of a lot of both endogenous and exogenous factors (i.e., age, sex, genetic background, inflammation, hormones, drugs, diet, exercise, hematological analyzers, and ranges of values), modulating the biology and physiology of erythrocytes. Thus, the singular monitoring of RDW cannot be used to predict cardiovascular disorders. Accordingly, we have reviewed the evidence for potential relationship of RDW values with alterations in the cardiovascular system (i.e., regenerative capacity, endothelial turnover, and senescence of cardiovascular cells), associated with vascular aging and disease. In addition, we highlight the inevitable impact of biases in clinical application of RDW related to CVDs. Based on our thorough review of literature, we suggest a combined evaluation of RDW with other emerging biomarkers related to vascular aging and the diagnosis and prognosis of CVDs, including telomere length of leukocytes, circulating nucleated red blood cells (nRBCs) and endothelial progenitor cells (EPCs) in future large scale studies.
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Affiliation(s)
- Donatella Poz
- 1 Department of Laboratory Medicine, Institute of Clinical Pathology, Azienda Sanitaria Universitaria Integrata (ASUI) di Udine, Udine, Italy
| | - Elena De Falco
- 2 Department of Medical-Surgical Sciences and Biotechnologies, "Sapienza" University of Rome, Latina, Italy
| | - Calogera Pisano
- 3 Cardiac Surgery, Tor Vergata University, Cardiochirurgia Policlinico Tor Vergata, Rome, Italy
| | - Rosalinda Madonna
- 4 Heart Failure Research, Texas Heart Institute, St. Luke's Episcopal Hospital, Houston, Texas.,5 Department of Internal Medicine, Cardiology, The University of Texas Health Science Center at Houston, Houston, Texas.,6 Department of Neurosciences, Center of Aging Sciences and Translational Medicine, CESI-Met and Institute of Cardiology, Imaging and Clinical Sciences "G. D'Annunzio" University, Chieti, Italy
| | - Peter Ferdinandy
- 7 Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,8 Pharmahungary Group, Szeged, Hungary
| | - Carmela Rita Balistreri
- 9 Department of Pathobiology and Medical and Forensic Biotechnologies, University of Palermo, Palermo, Italy
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