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Antwi EB, Olins A, Teif VB, Bieg M, Bauer T, Gu Z, Brors B, Eils R, Olins D, Ishaque N. Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biol Open 2020; 9:bio044222. [PMID: 31988093 PMCID: PMC7044446 DOI: 10.1242/bio.044222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenomic regulation plays a vital role in cell differentiation. The leukemic HL-60/S4 [human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306)] promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its differentiation. We performed whole-genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential Cytosine-phosphate-Guanine dinucleotide methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune-related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed the strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large-scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation.
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Affiliation(s)
- Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular and Cellular Engineering, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg, Germany
| | - Ada Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Colchester, UK
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Donald Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
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Afford SC, Kakoullis T, Oates J, Crocker J, Strain AJ. Effects of hepatocyte growth factor on differentiation and cMET receptor expression in the promyelocytic HL60 cell line. Mol Pathol 2010; 48:M23-7. [PMID: 16695971 PMCID: PMC407915 DOI: 10.1136/mp.48.1.m23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Aim-To determine the effects of hepatocyte growth factor (HGF) on myeloid cell differentiation and cMET expression using the promyelocytic HL60 cell line.Methods-HL60 cells cultured with purified recombinant HGF, dimethyl sulphoxide (DMSO), or 12-O tetradecanoylphorbol-13-acetate (TPA) were immunostained for the differentiation markers, human neutrophil elastase (HNE), cathepsin B, MAC387, or the receptor for hepatocyte growth factor (cMET).Results-HGF treated cells were positive on staining for cathepsin B and MAC387, but were negative for HNE, indicating monocytic differentiation. HGF treated cells had the morphology of monocytes but continued to divide at the same rate as control cells and remained non-adherent. DMSO treated cells were positive for HNE and cell numbers were reduced, confirming myeloid differentiation. TPA treated cells were positive for cathepsin B and MAC387, cell numbers were reduced, and the cells became adherent, confirming terminal monocytic differentiation. Untreated HL60 cells were weakly positive for cMET at the start of the culture period and expression increased after 72 hours. Cells treated with HGF, DMSO, or TPA were also positive for cMET.Conclusions-These data suggest that HGF induced partial monocytic differentiation in HL60 cells. In addition, expression of cMET by HL60 cells occurs at an early stage in myelomonocytic cells and is maintained after differentiation along either the myeloid or monocytic pathways.
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Affiliation(s)
- S C Afford
- The Liver Research Laboratories, Queen Elizabeth Hospital, Edgbaston, Birmingham B15 2TH
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