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Ginoudis A, Ioannidou S, Tsakiroglou G, Kazeli K, Vagdatli E, Lymperaki E. Correlation of Albumin, Red Cell Distribution Width and Other Biochemical and Hematological Parameters with Glycated Hemoglobin in Diabetic, Prediabetic and Non-Diabetic Patients. Int J Mol Sci 2024; 25:8037. [PMID: 39125606 PMCID: PMC11311434 DOI: 10.3390/ijms25158037] [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: 07/03/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Diabetes mellitus is a chronic metabolic disease that affects more than 10.5% of the world's adult population. Biochemical and hematological parameters, such as albumin (ALB) and red cell distribution width (RDW), have been shown to be altered in diabetic patients. This study aimed to correlate hematological and biochemical parameters with glycated hemoglobin (HbA1c). A total of 777 adults (372 women and 405 men, aged 19-85 years) were divided into three groups: 218 participants with HbA1c < 5.7% (group A: non-diabetic), 226 with HbA1c ≥ 5.7% and <6.5% (group B: prediabetic) and 333 with HbA1c ≥ 6.5% (group C: diabetic). Biochemical and hematological parameters were compared among the three groups. An analysis of variance was performed to determine the correlations of the parameters among the groups. The ALB and sodium (Na) levels were significantly lower in group C than in groups A (ALB: 3.8 g/dL vs. 4.1 g/dL, p < 0.0001, Na: 138.4 mmol/L vs. 139.3 mmol/L, p < 0.001) and B (ALB: 3.8 g/dL vs. 4.0 g/dL, p < 0.0001, Na: 138.4 mmol/L vs. 139.6 mmol/L, p < 0.0001), whereas the RDW-standard deviation (RDW-SD) and urea were increased in group C as compared to group A (RDW: 45.8 vs. 43.9 fL, p < 0.0001, urea: 55.6 mg/dL vs. 38.5 mg/dL, p < 0.0001). The mean platelet volume (MPV) was increased in group C as compared to group A (9.3 fL vs. 9.1 fL, p < 0.05, respectively). Τhe increase in RDW-SD in group A as compared to B and C demonstrates the impact of hyperglycemia on red blood cells. Albumin and RDW might improve risk assessment for the development of diabetes. These results highlight the potential role of these parameters as an indication for prediabetes that would alert for measurement of HbA1c.
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Affiliation(s)
- Argyrios Ginoudis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Stavroula Ioannidou
- Department of Biomedical Sciences, International Hellenic University, 57400 Thessaloniki, Greece; (S.I.); (G.T.); (K.K.); (E.V.)
| | - Georgia Tsakiroglou
- Department of Biomedical Sciences, International Hellenic University, 57400 Thessaloniki, Greece; (S.I.); (G.T.); (K.K.); (E.V.)
| | - Konstantina Kazeli
- Department of Biomedical Sciences, International Hellenic University, 57400 Thessaloniki, Greece; (S.I.); (G.T.); (K.K.); (E.V.)
| | - Eleni Vagdatli
- Department of Biomedical Sciences, International Hellenic University, 57400 Thessaloniki, Greece; (S.I.); (G.T.); (K.K.); (E.V.)
- Hippokration General Hospital of Thessaloniki, 54642 Thessaloniki, Greece
| | - Evgenia Lymperaki
- Department of Biomedical Sciences, International Hellenic University, 57400 Thessaloniki, Greece; (S.I.); (G.T.); (K.K.); (E.V.)
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Peters MAE, King AA, Wale N. Red blood cell dynamics during malaria infection challenge the assumptions of mathematical models of infection dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575051. [PMID: 38260611 PMCID: PMC10802624 DOI: 10.1101/2024.01.10.575051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
For decades, mathematical models have been used to understand the course and outcome of malaria infections (i.e., infection dynamics) and the evolutionary dynamics of the parasites that cause them. A key conclusion of these models is that red blood cell (RBC) availability is a fundamental driver of infection dynamics and parasite trait evolution. The extent to which this conclusion holds will in part depend on model assumptions about the host-mediated processes that regulate RBC availability i.e., removal of uninfected RBCs and supply of RBCs. Diverse mathematical functions have been used to describe host-mediated RBC supply and clearance, but it remains unclear whether they adequately capture the dynamics of RBC supply and clearance during infection. Here, we use a unique dataset, comprising time-series measurements of erythrocyte (i.e., mature RBC) and reticulocyte (i.e., newly supplied RBC) densities during Plasmodium chabaudi malaria infection, and a quantitative data-transformation scheme to elucidate whether RBC dynamics conform to common model assumptions. We found that RBC clearance and supply are not well described by mathematical functions commonly used to model these processes. Furthermore, the temporal dynamics of both processes vary with parasite growth rate in a manner again not captured by existing models. Together, these finding suggest that new model formulations are required if we are to explain and ultimately predict the within-host population dynamics and evolution of malaria parasites.
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Sun N, Wang Z, Jiang H, Wang B, Du K, Huang C, Wang C, Yang T, Wang Y, Liu Y, Wang L. Angelica sinensis polysaccharides promote extramedullary stress erythropoiesis via ameliorating splenic glycolysis and EPO/STAT5 signaling-regulated macrophages. J Mol Histol 2024:10.1007/s10735-024-10219-z. [PMID: 38969952 DOI: 10.1007/s10735-024-10219-z] [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: 04/04/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
Conventional treatments exhibit various side effects on chronic stress anemia. Extramedullary stress erythropoiesis is a compensatory mechanism, which may effectively counteract anemia. Angelica sinensis polysaccharides (ASP) are the main active ingredient found in Angelica sinensis and exhibit antioxidant and hematopoietic effects. However, the effects of ASP on extramedullary stress erythropoiesis remain to be unclear. Here, we demonstrated the protective effects of ASP on chemotherapeutic drug 5-fluorouracil (5-FU)-induced decline in peripheral blood parameters such as RBC counts, HGB, HCT, and MCH, and the decline of BFU-E colony enumeration in the bone marrow. Meanwhile, ASP promoted extramedullary erythropoiesis, increasing cellular proliferation in the splenic red pulp and cyclin D1 protein expression, abrogating phase G0/G1 arrest of c-kit+ cells in mouse spleen. RT-qPCR and immunohistochemistry further revealed that ASP increased macrophage chemokine Ccl2 genetic expression and the number of F4/80+ macrophages in the spleen. The colony-forming assay showed that ASP significantly increased splenic BFU-E. Furthermore, we found that ASP facilitated glycolytic genes including Hk2, Pgk1, Pkm, Pdk1, and Ldha via PI3K/Akt/HIF2α signaling in the spleen. Subsequently, ASP declined pro-proinflammatory factor IL-1β, whereas upregulating erythroid proliferation-associated genes Gdf15, Bmp4, Wnt2b, and Wnt8a. Moreover, ASP facilitated EPO/STAT5 signaling in splenic macrophages, thus enhancing erythroid lineage Gata2 genetic expression. Our study indicated that ASP may improve glycolysis, promoting the activity of splenic macrophages, subsequently promoting erythroid progenitor cell expansion. Additionally, ASP facilitates erythroid differentiation via macrophage-mediated EpoR/STAT5 signaling; suggesting it might be a promising strategy for stress anemia treatment.
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Affiliation(s)
- Nianci Sun
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Ziling Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Honghui Jiang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Biyao Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Kunhang Du
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Caihong Huang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Cheng Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Yang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yaping Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yafei Liu
- Chongqing University Jiangjin Hospital, Chongqing, China.
| | - Lu Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China.
- Department of Histology and Embryology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China.
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Ma JK, Su LD, Feng LL, Li JL, Pan L, Danzeng Q, Li Y, Shang T, Zhan XL, Chen SY, Ying S, Hu JR, Chen XQ, Zhang Q, Liang T, Lu XJ. TFPI from erythroblasts drives heme production in central macrophages promoting erythropoiesis in polycythemia. Nat Commun 2024; 15:3976. [PMID: 38729948 PMCID: PMC11087540 DOI: 10.1038/s41467-024-48328-8] [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: 07/25/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Bleeding and thrombosis are known as common complications of polycythemia for a long time. However, the role of coagulation system in erythropoiesis is unclear. Here, we discover that an anticoagulant protein tissue factor pathway inhibitor (TFPI) plays an essential role in erythropoiesis via the control of heme biosynthesis in central macrophages. TFPI levels are elevated in erythroblasts of human erythroblastic islands with JAK2V617F mutation and hypoxia condition. Erythroid lineage-specific knockout TFPI results in impaired erythropoiesis through decreasing ferrochelatase expression and heme biosynthesis in central macrophages. Mechanistically, the TFPI interacts with thrombomodulin to promote the downstream ERK1/2-GATA1 signaling pathway to induce heme biosynthesis in central macrophages. Furthermore, TFPI blockade impairs human erythropoiesis in vitro, and normalizes the erythroid compartment in mice with polycythemia. These results show that erythroblast-derived TFPI plays an important role in the regulation of erythropoiesis and reveal an interplay between erythroblasts and central macrophages.
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Affiliation(s)
- Jun-Kai Ma
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li-Da Su
- Neuroscience Care Unit, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Lin-Lin Feng
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Jing-Lin Li
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li Pan
- The General Hospital of Tibet Military Area Command, Lhasa, China
| | - Qupei Danzeng
- Department of Tibetan Medicine; University of Tibetan Medicine, Lhasa, 540100, China
| | - Yanwei Li
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Tongyao Shang
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiao-Lin Zhan
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Si-Ying Chen
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Shibo Ying
- School of Public Health, Hangzhou Medical College, Hangzhou, 310013, China
| | - Jian-Rao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xue Qun Chen
- Zhejiang University, School of Brain Science and Brain Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Xin-Jiang Lu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Nazarov K, Perik-Zavodskii R, Perik-Zavodskaia O, Alrhmoun S, Volynets M, Shevchenko J, Sennikov S. Phenotypic Alterations in Erythroid Nucleated Cells of Spleen and Bone Marrow in Acute Hypoxia. Cells 2023; 12:2810. [PMID: 38132130 PMCID: PMC10741844 DOI: 10.3390/cells12242810] [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: 11/13/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
Hypoxia leads to metabolic changes at the cellular, tissue, and organismal levels. The molecular mechanisms for controlling physiological changes during hypoxia have not yet been fully studied. Erythroid cells are essential for adjusting the rate of erythropoiesis and can influence the development and differentiation of immune cells under normal and pathological conditions. We simulated high-altitude hypoxia conditions for mice and assessed the content of erythroid nucleated cells in the spleen and bone marrow under the existing microenvironment. For a pure population of CD71+ erythroid cells, we assessed the production of cytokines and the expression of genes that regulate the immune response. Our findings show changes in the cellular composition of the bone marrow and spleen during hypoxia, as well as changes in the composition of the erythroid cell subpopulations during acute hypoxic exposure in the form of a decrease in orthochromatophilic erythroid cells that are ready for rapid enucleation and the accumulation of their precursors. Cytokine production normally differs only between organs; this effect persists during hypoxia. In the bone marrow, during hypoxia, genes of the C-lectin pathway are activated. Thus, hypoxia triggers the activation of various adaptive and compensatory mechanisms in order to limit inflammatory processes and modify metabolism.
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Affiliation(s)
- Kirill Nazarov
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
| | - Roman Perik-Zavodskii
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
| | - Olga Perik-Zavodskaia
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
| | - Saleh Alrhmoun
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina Volynets
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Julia Shevchenko
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
| | - Sergey Sennikov
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology”, 630099 Novosibirsk, Russia; (K.N.); (R.P.-Z.); (O.P.-Z.); (S.A.); (M.V.); (J.S.)
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Teofili L, Papacci P, Giannantonio C, Bianchi M, Giovanna Valentini C, Vento G. Allogenic Cord Blood Transfusion in Preterm Infants. Clin Perinatol 2023; 50:881-893. [PMID: 37866854 DOI: 10.1016/j.clp.2023.07.005] [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] [Indexed: 10/24/2023]
Abstract
Repeated red blood cell (RBC) transfusions in preterm neonates cause the progressive displacement of fetal hemoglobin (HbF) by adult hemoglobin. The ensuing increase of oxygen delivery may result at the cellular level in a dangerous condition of hyperoxia, explaining the association between low-HbF levels and retinopathy of prematurity or bronchopulmonary dysplasia. Transfusing preterm neonates with RBC concentrates obtained from allogeneic umbilical blood is a strategy to increase hemoglobin concentration without depleting the physiologic HbF reservoir. This review summarizes the mechanisms underlying a plausible beneficial impact of this strategy and reports clinical experience gathered so far in this field.
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Affiliation(s)
- Luciana Teofili
- Transfusion Medicine Department, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo Gemelli 8, Rome, Italy.
| | - Patrizia Papacci
- Neonatal Intensive Care Unit, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo Gemelli 8, Rome, Italy
| | - Carmen Giannantonio
- Neonatal Intensive Care Unit, Fondazione Policlinico A. Gemelli IRCCS, Largo Gemelli 8, Rome, Italy
| | - Maria Bianchi
- Transfusion Medicine Department, Fondazione Policlinico A. Gemelli IRCCS, Largo Gemelli 8, Rome, Italy
| | | | - Giovanni Vento
- Neonatal Intensive Care Unit, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo Gemelli 8, Rome, Italy
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Kim I, Park T, Noh JY, Kim W. Emerging role of Hippo pathway in the regulation of hematopoiesis. BMB Rep 2023; 56:417-425. [PMID: 37574808 PMCID: PMC10471462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023] Open
Abstract
In various organisms, the Hippo signaling pathway has been identified as a master regulator of organ size determination and tissue homeostasis. The Hippo signaling coordinates embryonic development, tissue regeneration and differentiation, through regulating cell proliferation and survival. The YAP and TAZ (YAP/TAZ) act as core transducers of the Hippo pathway, and they are tightly and exquisitely regulated in response to various intrinsic and extrinsic stimuli. Abnormal regulation or genetic variation of the Hippo pathway causes a wide range of human diseases, including cancer. Recent studies have revealed that Hippo signaling plays a pivotal role in the immune system and cancer immunity. Due to pathophysiological importance, the emerging role of Hippo signaling in blood cell differentiation, known as hematopoiesis, is receiving much attention. A number of elegant studies using a genetically engineered mouse (GEM) model have shed light on the mechanistic and physiological insights into the Hippo pathway in the regulation of hematopoiesis. Here, we briefly review the function of Hippo signaling in the regulation of hematopoiesis and immune cell differentiation. [BMB Reports 2023; 56(8): 417-425].
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Affiliation(s)
- Inyoung Kim
- Department of Biochemistry, Chungnam National University, Daejeon 34134, Korea
| | - Taeho Park
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science & Technology (UST), Daejeon 34113, Korea
| | - Ji-Yoon Noh
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science & Technology (UST), Daejeon 34113, Korea
| | - Wantae Kim
- Department of Biochemistry, Chungnam National University, Daejeon 34134, Korea
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Bina M. Defining Candidate Imprinted loci in Bos taurus. Genes (Basel) 2023; 14:1036. [PMID: 37239396 PMCID: PMC10217866 DOI: 10.3390/genes14051036] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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