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Kidder BL. Decoding the universal human chromatin landscape through teratoma-based profiling. Nucleic Acids Res 2024; 52:3589-3606. [PMID: 38281248 PMCID: PMC11039989 DOI: 10.1093/nar/gkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Teratoma formation is key for evaluating differentiation of human pluripotent stem cells into embryonic germ layers and serves as a model for understanding stem cell differentiation and developmental processes. Its potential for insights into epigenome and transcriptome profiling is significant. This study integrates the analysis of the epigenome and transcriptome of hESC-generated teratomas, comparing transcriptomes between hESCs and teratomas. It employs cell type-specific expression patterns from single-cell data to deconvolve RNA-Seq data and identify cell types within teratomas. Our results provide a catalog of activating and repressive histone modifications, while also elucidating distinctive features of chromatin states. Construction of an epigenetic signature matrix enabled the quantification of diverse cell populations in teratomas and enhanced the ability to unravel the epigenetic landscape in heterogeneous tissue contexts. This study also includes a single cell multiome atlas of expression (scRNA-Seq) and chromatin accessibility (scATAC-Seq) of human teratomas, further revealing the complexity of these tissues. A histology-based digital staining tool further complemented the annotation of cell types in teratomas, enhancing our understanding of their cellular composition. This research is a valuable resource for examining teratoma epigenomic and transcriptomic landscapes and serves as a model for epigenetic data comparison.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
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Kidder BL, Ruden X, Singh A, Marben TA, Rass L, Chakravarty A, Xie Y, Puscheck EE, Awonuga AO, Harris S, Ruden DM, Rappolee DA. Novel high throughput screen reports that benzo(a)pyrene overrides mouse trophoblast stem cell multipotency, inducing SAPK activity, HAND1 and differentiated trophoblast giant cells. Placenta 2024:S0143-4004(23)00644-6. [PMID: 38245404 DOI: 10.1016/j.placenta.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
INTRODUCTION Cultured mouse trophoblast stem cells (mTSC) maintain proliferation/normal stemness (NS) under FGF4, which when removed, causes normal differentiation (ND). Hypoxic, or hyperosmotic stress forces trophoblast giant cells (TGC) differentiate. Hypoxic, hyperosmotic, and genotoxic benzo(a)pyrene (BaP), which is found in tobacco smoke, force down-regulation of inhibitor of differentiation (Id)2, enabling TGC differentiation. Hypoxic and hyperosmotic stress induce TGC by SAPK-dependent HAND1 increase. Here we test whether BaP forces mTSC-to-TGC while inducing SAPK and HAND1. METHODS Hand1 and SAPK activity were assayed by immunoblot, mTSC-to-TGC growth and differentiation were assayed at Tfinal after 72hr exposure of BaP, NS, ND, Retinoic acid (RA), or sorbitol. Nuclear-stained cells were micrographed automatically by a live imager, and assayed by ImageJ/FIJI, Biotek Gen 5, AIVIA proprietary artificial intelligence (AI) software or open source, CellPose artificial intelligence/AI software. RESULTS BaP (0.05-1μM) activated SAPK and HAND1 without diminishing growth. TSC-to-TGC differentiation was assayed with increasingly accuracy for 2-4 N cycling nuclei and >4 N differentiating TGC nuclei, using ImageJ/FIJI, Gen 5, AIVIA, or CellPose AI software. The AIVIA and Cellpose AI software matches human accuracy. The lowest BaP effects on SAPK activation/HAND1 increase are >10-fold more sensitive than similar effects for mESC. RA induces 44-47% 1st lineage TGC differentiation, but the same RA dose induces only 1% 1st lineage mESC differentiation. DISCUSSION First, these pilot data suggest that mTSC can be used in high throughput screens (HTS) to predict toxicant exposures that force TGC differentiation. Second, mTSC differentiated more cells than mESC for similar stress exposures, Third, open source AI can replace human micrograph quantitation and enable a miscarriage-predicting HTS.
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Affiliation(s)
- B L Kidder
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - X Ruden
- CS Mott Center/WSU Ob/gyn Department, USA; Reproductive Stress Inc, Grosse Pointe Farms, MI, USA
| | - A Singh
- CS Mott Center/WSU Ob/gyn Department, USA; WSU CMMG, USA
| | - T A Marben
- University of Detroit, Mercy (NIH Build Fellow), USA
| | - L Rass
- Barber Foundation Fellows/WSU, USA
| | | | - Y Xie
- Western Fertility, Los Angeles, CA, USA
| | - E E Puscheck
- CS Mott Center/WSU Ob/gyn Department, USA; Invia Infertility, Chicago, IL, USA
| | | | - S Harris
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - D M Ruden
- CS Mott Center/WSU Ob/gyn Department, USA; IEHS, WSU, USA
| | - D A Rappolee
- CS Mott Center/WSU Ob/gyn Department, USA; Reproductive Stress Inc, Grosse Pointe Farms, MI, USA; Dept of Physiology, WSU, USA.
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Kurup JT, Kim S, Kidder BL. Identifying Cancer Type-Specific Transcriptional Programs through Network Analysis. Cancers (Basel) 2023; 15:4167. [PMID: 37627195 PMCID: PMC10453000 DOI: 10.3390/cancers15164167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Identifying cancer type-specific genes that define cell states is important to develop effective therapies for patients and methods for detection, early diagnosis, and prevention. While molecular mechanisms that drive malignancy have been identified for various cancers, the identification of cell-type defining transcription factors (TFs) that distinguish normal cells from cancer cells has not been fully elucidated. Here, we utilized a network biology framework, which assesses the fidelity of cell fate conversions, to identify cancer type-specific gene regulatory networks (GRN) for 17 types of cancer. Through an integrative analysis of a compendium of expression data, we elucidated core TFs and GRNs for multiple cancer types. Moreover, by comparing normal tissues and cells to cancer type-specific GRNs, we found that the expression of key network-influencing TFs can be utilized as a survival prognostic indicator for a diverse cohort of cancer patients. These findings offer a valuable resource for exploring cancer type-specific networks across a broad range of cancer types.
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Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Jacob JB, Wei KC, Bepler G, Reyes JD, Cani A, Polin L, White K, Kim S, Viola N, McGrath J, Guastella A, Yin C, Mi QS, Kidder BL, Wagner KU, Ratner S, Phillips V, Xiu J, Parajuli P, Wei WZ. Identification of Actionable Targets for Breast Cancer Intervention Using a Diversity Outbred Mouse Model. iScience 2023; 26:106320. [PMID: 36968078 PMCID: PMC10034465 DOI: 10.1016/j.isci.2023.106320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/16/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
HER2-targeted therapy has improved breast cancer survival, but treatment resistance and disease prevention remain major challenges. Genes that enable HER2/Neu oncogenesis are the next intervention targets. A bioinformatics discovery platform of HER2/Neu-expressing Diversity Outbred (DO) F1 Mice was established to identify cancer-enabling genes. Quantitative Trait Loci (QTL) associated with onset ages and growth rates of spontaneous mammary tumors were sought. Twenty-six genes in 3 QTL contain sequence variations unique to the genetic backgrounds that are linked to aggressive tumors and 21 genes are associated with human breast cancer survival. Concurrent identification of TSC22D3, a transcription factor, and its target gene LILRB4, a myeloid cell checkpoint receptor, suggests an immune axis for regulation, or intervention, of disease. We also investigated TIEG1 gene that impedes tumor immunity but suppresses tumor growth. Although not an actionable target, TIEG1 study revealed genetic regulation of tumor progression, forming the basis of the genetics-based discovery platform.
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Affiliation(s)
- Jennifer B. Jacob
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Kuang-Chung Wei
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Gerold Bepler
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Joyce D. Reyes
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Andi Cani
- Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lisa Polin
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Kathryn White
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Seongho Kim
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Nerissa Viola
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Julie McGrath
- Clinical and Translational Research, Caris Life Sciences, Irving, TX75039, USA
| | - Anthony Guastella
- Clinical and Translational Research, Caris Life Sciences, Irving, TX75039, USA
| | - CongCong Yin
- Department of Immunology, Henry Ford Health System, Detroit, MI48202, USA
| | - Qing-Shen Mi
- Department of Immunology, Henry Ford Health System, Detroit, MI48202, USA
| | - Benjamin L. Kidder
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Kay-Uwe Wagner
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Stuart Ratner
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Victoria Phillips
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Joanne Xiu
- Clinical and Translational Research, Caris Life Sciences, Irving, TX75039, USA
| | - Prahlad Parajuli
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
| | - Wei-Zen Wei
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA
- Corresponding author
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Kurup JT, Han Z, Jin W, Kidder BL. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development 2020; 147:dev.188516. [PMID: 33144397 DOI: 10.1242/dev.188516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022]
Abstract
Heterochromatin, a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification H4K20me3 or the histone methyltransferase SUV420H2 regulates embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near-complete loss of H4K20me3 genome wide, dysregulated gene expression and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale chromatin interactions in pluripotent ES cells. Our results indicate that SUV420H2 plays a crucial role in stabilizing the three-dimensional chromatin landscape of ES cells, as loss of SUV420H2 resulted in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin and surrounding regions, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene-regulatory regions. Together, these findings describe a new role for SUV420H2 in regulating the chromatin landscape of ES cells.
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Affiliation(s)
- Jiji T Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhijun Han
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Kidder BL. Simultaneous Derivation of Embryonic and Trophoblast Stem Cells from Mouse Blastocysts. Methods Mol Biol 2020; 2117:235-241. [PMID: 31960383 DOI: 10.1007/978-1-0716-0301-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The formation of the blastocyst during mammalian development involves the segregation of two populations of cells with unequal potential: pluripotent cells of the inner cell mass (ICM) and multipotent cells of the trophectoderm (TE). ICM cells maintain the capacity to give rise to all cells represented in the organism, while TE cells, which represent the first lineage to emerge during development, are capable of differentiating into trophoblast lineages of the placenta. The ICM and TE are both essential for development. The ICM is genetically programmed to generate all cells of the embryo proper, while the TE forms extraembryonic trophoblast lineages and is required for implantation of the embryo and maternal-fetal exchange of nutrients and waste. Embryonic stem (ES) cells, which can be derived from the ICM of blastocysts in the presence of external signals such as LIF, can self-renewal indefinitely, and because they can differentiate into all cells of the organism, ES cells are a widely used in vitro model to study genetics and development. Trophoblast stem (TS) cells can be derived from the TE of blastocyst stage embryos in the presence of FGF4, and like ES cells, TS cells are also able to self-renew indefinitely. Because TS cells can differentiate into epithelial lineages of the trophoblast, TS cells are an ideal in vitro model to study the biology of the trophoblast. In this chapter, we describe protocols for simultaneous derivation of ES cells and TS cells from mouse blastocysts and culture conditions that promote self-renewal of hybrid ESC/TSC colonies. These protocols are sufficient for efficient derivation of hybrid ESC/TSC colonies.
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Affiliation(s)
- Benjamin L Kidder
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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Abstract
Trophoblast cells are the first committed lineage to emerge during mammalian preimplantation embryo development. Trophoblast stem (TS) cells can be derived from the trophectoderm (TE) of blastocyst-stage embryos and differentiate into extraembryonic trophoblast cells of the placenta. While mouse TS cells are an indispensable tool to study placental development, and reproductive diseases such as implantation failure and recurrent miscarriage, human TS cells have not been isolated. To model human trophoblast development and to investigate trophoblast-specific causes of reproductive diseases, it will be important to derive human induced trophoblast stem (iTS) cells. Recent studies have shown that fibroblasts can be reprogrammed to iTS cells by overexpressing four transcription factors (TFs) including TFAP2C, GATA3, EOMES, and ETS2. Here, we describe a protocol to directly convert mouse embryonic fibroblasts (MEFs) to iTS cells following overexpression of 10 TFs. iTS cells are capable of self-renewing using conventional TS cell culture media supplemented with the external signal FGF4 and heparin. iTS cells are also able to differentiate into trophoblast lineages.
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Affiliation(s)
- Benjamin L Kidder
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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8
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Kidder BL. Derivation of LIF-Independent Embryonic Stem Cells Using Inducible OCT4 Expression. Methods Mol Biol 2020; 2117:229-234. [PMID: 31960382 DOI: 10.1007/978-1-0716-0301-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pluripotent mouse embryonic stem (ES) cells, which are derived from the inner cell mass (ICM) of preimplantation stage embryos, are capable of self-renewing indefinitely in the presence of the external signal leukemia inhibitory factor (LIF), activation of Wnt signaling through inhibition of GSK3, and inhibition of MAP kinase/ERK kinase signaling. The OCT4 transcription factor is expressed highly in pluripotent cells and is a central transcriptional regulator of the pluripotent state. Here, we describe a protocol to culture ES cells in LIF-independent and serum-free media using an inducible OCT4 (iOCT4) ES cell model system. This protocol is sufficient to sustain ES cell self-renewal in vitro in defined conditions in the absence of external signals. LIF-independent iOCT4 ES cells are fully capable of differentiating following deactivation of the inducible OCT4 transgene.
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Affiliation(s)
- Benjamin L Kidder
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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Zhang Q, Thakur C, Fu Y, Bi Z, Wadgaonkar P, Xu L, Liu Z, Liu W, Wang J, Kidder BL, Chen F. Mdig promotes oncogenic gene expression through antagonizing repressive histone methylation markers. Theranostics 2020; 10:602-614. [PMID: 31903140 PMCID: PMC6929976 DOI: 10.7150/thno.36220] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022] Open
Abstract
The mineral dust-induced gene (mdig) is overexpressed in a number of human cancers, suggesting critical roles of this gene played on the pathogenesis of cancers. Unlike several other JmjC-domain containing proteins that exhibit histone demethylase activity, it remains enigmatic whether mdig is involved in the demethylation processes of the histone proteins. Methods: To provide direct evidence suggesting contribution of mdig to the demethylation of histone proteins, we recently examined the histone methylation profiles in human bronchial epithelial cells as well as two cancer cell lines with mdig knockout through CRISPR-Cas9 gene editing. Results: Global histone methylation analysis revealed a pronounced increase of the repressive histone trimethylation in three different cell types with mdig depletion, including trimethylation of lysines 9 and 27 on histone H3 (H3K9me3, H3K27me3) and trimethylation of lysine 20 of histone H4 (H4K20me3). Importantly, data from both ChIP-seq and RNA-seq suggested that genetic disruption of mdig enriches repressive histone trimethylation and inhibits expression of target genes in the oncogenic pathways of cell growth, stemness of the cells, tissue fibrosis, and cell motility. Conclusion: Taken together, our study provides the first insight into the molecular effects of mdig as an antagonist for repressive histone methylation markers and suggests that targeting mdig may represent a new area to explore in cancer therapy.
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Affiliation(s)
- Qian Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Chitra Thakur
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Yao Fu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Zhuoyue Bi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Priya Wadgaonkar
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Liping Xu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Zhipeng Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W. Stadium Avenue, West Lafayette, IN 47907, USA
| | - Wanqing Liu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W. Stadium Avenue, West Lafayette, IN 47907, USA
- Department of Pharmacology, School of Medicine, Wayne State University, 540 E. Canfield Street, Detroit, MI 48201, USA
| | - Jian Wang
- Department of Pathology, School of Medicine, Wayne State University, 540 E. Canfield Street, Detroit, MI 48201, USA
| | - Benjamin L. Kidder
- Department of Oncology and the Karmanos Cancer Institute, School of Medicine, Wayne State University, 4100 John R Street, Detroit, MI 48201, USA
| | - Fei Chen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
- Department of Oncology and the Karmanos Cancer Institute, School of Medicine, Wayne State University, 4100 John R Street, Detroit, MI 48201, USA
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Vizcardo R, Klemen ND, Islam SMR, Gurusamy D, Tamaoki N, Yamada D, Koseki H, Kidder BL, Yu Z, Jia L, Henning AN, Good ML, Bosch-Marce M, Maeda T, Liu C, Abdullaev Z, Pack S, Palmer DC, Stroncek DF, Ito F, Flomerfelt FA, Kruhlak MJ, Restifo NP. Generation of Tumor Antigen-Specific iPSC-Derived Thymic Emigrants Using a 3D Thymic Culture System. Cell Rep 2019; 22:3175-3190. [PMID: 29562175 DOI: 10.1016/j.celrep.2018.02.087] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/08/2018] [Accepted: 02/22/2018] [Indexed: 01/04/2023] Open
Abstract
Induced pluripotent stem cell (iPSC)-derived T cells may provide future therapies for cancer patients, but those generated by current methods, such as the OP9/DLL1 system, have shown abnormalities that pose major barriers for clinical translation. Our data indicate that these iPSC-derived CD8 single-positive T cells are more like CD4+CD8+ double-positive T cells than mature naive T cells because they display phenotypic markers of developmental arrest and an innate-like phenotype after stimulation. We developed a 3D thymic culture system to avoid these aberrant developmental fates, generating a homogeneous subset of CD8αβ+ antigen-specific T cells, designated iPSC-derived thymic emigrants (iTEs). iTEs exhibit phenotypic and functional similarities to naive T cells both in vitro and in vivo, including the capacity for expansion, memory formation, and tumor suppression. These data illustrate the limitations of current methods and provide a tool to develop the next generation of iPSC-based antigen-specific immunotherapies.
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Affiliation(s)
- Raul Vizcardo
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Nicholas D Klemen
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - S M Rafiqul Islam
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Devikala Gurusamy
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Naritaka Tamaoki
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daisuke Yamada
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa 230-0045, Japan
| | - Benjamin L Kidder
- Department of Oncology and Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Li Jia
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Amanda N Henning
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Meghan L Good
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Marta Bosch-Marce
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Takuya Maeda
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Zied Abdullaev
- Experimental Pathology Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Svetlana Pack
- Experimental Pathology Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Douglas C Palmer
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David F Stroncek
- Department of Transfusion Medicine Department, Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Fumito Ito
- Department of Surgical Oncology, Roswell Park Cancer Center, Buffalo, NY 14263, USA; Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Francis A Flomerfelt
- Experimental Transplantation and Immunology Branch, NIH Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nicholas P Restifo
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Center for Cell-Based Therapy, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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11
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Kurup JT, Campeanu IJ, Kidder BL. Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing. Epigenetics Chromatin 2019; 12:20. [PMID: 30940185 PMCID: PMC6444878 DOI: 10.1186/s13072-019-0266-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone 3 lysine 4 (H3K4) demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. RESULTS Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. CONCLUSION Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.
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Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Ion J. Campeanu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
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12
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Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol 2018; 57:79-85. [PMID: 30448242 DOI: 10.1016/j.semcancer.2018.11.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling stem cell function and tumorigenesis. The histone lysine demethylase, KDM5B, which catalyzes the demethylation of histone 3 lysine 4 (H3K4), is important for embryonic stem (ES) cell differentiation, and is a critical regulator of the H3K4-methylome during early mouse embryonic pre-implantation stage development. KDM5B is also overexpressed, amplified, or mutated in many cancer types. In cancer cells, KDM5B regulates expression of oncogenes and tumor suppressors by modulating H3K4 methylation levels. In this review, we examine how KDM5B regulates gene expression and cellular fates of stem cells and cancer cells by temporally and spatially controlling H3K4 methylation levels.
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Affiliation(s)
- Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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13
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Rosati R, Polin L, Ducker C, Li J, Bao X, Selvakumar D, Kim S, Xhabija B, Larsen M, McFall T, Huang Y, Kidder BL, Fribley A, Saxton J, Kakuta H, Shaw P, Ratnam M. Strategy for Tumor-Selective Disruption of Androgen Receptor Function in the Spectrum of Prostate Cancer. Clin Cancer Res 2018; 24:6509-6522. [PMID: 30185422 DOI: 10.1158/1078-0432.ccr-18-0982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/03/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Testosterone suppression in prostate cancer is limited by serious side effects and resistance via restoration of androgen receptor (AR) functionality. ELK1 is required for AR-dependent growth in various hormone-dependent and castration-resistant prostate cancer models. The amino-terminal domain of AR docks at two sites on ELK1 to coactivate essential growth genes. This study explores the ability of small molecules to disrupt the ELK1-AR interaction in the spectrum of prostate cancer, inhibiting AR activity in a manner that would predict functional tumor selectivity. EXPERIMENTAL DESIGN Small-molecule drug discovery and extensive biological characterization of a lead compound. RESULTS We have discovered a lead molecule (KCI807) that selectively disrupts ELK1-dependent promoter activation by wild-type and variant ARs without interfering with ELK1 activation by ERK. KCI807 has an obligatory flavone scaffold and functional hydroxyl groups on C5 and C3'. KCI807 binds to AR, blocking ELK1 binding, and selectively blocks recruitment of AR to chromatin by ELK1. KCI807 primarily affects a subset of AR target growth genes selectively suppressing AR-dependent growth of prostate cancer cell lines with a better inhibitory profile than enzalutamide. KCI807 also inhibits in vivo growth of castration/enzalutamide-resistant cell line-derived and patient-derived tumor xenografts. In the rodent model, KCI807 has a plasma half-life of 6 hours, and maintenance of its antitumor effect is limited by self-induced metabolism at its 3'-hydroxyl. CONCLUSIONS The results offer a mechanism-based therapeutic paradigm for disrupting the AR growth-promoting axis in the spectrum of prostate tumors while reducing global suppression of testosterone actions. KCI807 offers a good lead molecule for drug development.
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Affiliation(s)
- Rayna Rosati
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Lisa Polin
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Charles Ducker
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Jing Li
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Xun Bao
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Dakshnamurthy Selvakumar
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
- Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, Michigan
| | - Martha Larsen
- University of Michigan, Life Sciences Institute and Center for Chemical Genomics, Ann Arbor, Michigan
| | - Thomas McFall
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Yanfang Huang
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Andrew Fribley
- Department of Pediatrics, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Janice Saxton
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan
| | - Peter Shaw
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Manohar Ratnam
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan.
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14
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Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem 2018; 293:15120-15135. [PMID: 30115682 DOI: 10.1074/jbc.ra118.004974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/06/2022] Open
Abstract
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3- and H3K4me3-marked chromatin on a global scale in embryonic stem (ES) cells. We identified thousands of mRNAs and noncoding RNAs that associate with H4K20me3- and H3K4me3-marked chromatin. H4K20me3- and H3K4me3-interacting RNAs are involved in chromatin organization and modification and RNA processing, whereas H4K20me3-only RNAs are involved in cell motility and differentiation, and H3K4me3-only RNAs are involved in metabolic processes and RNA processing. Expression of H3K4me3-associated RNAs is enriched in ES cells, whereas expression of H4K20me3-associated RNAs is enriched in ES cells and differentiated cells. H4K20me3- and H3K4me3-interacting RNAs originate from genes that co-localize with features of active chromatin, including transcriptional machinery and active promoter regions, and the histone modification H3K36me3 in gene body regions. We also found that H4K20me3 and H3K4me3 are associated with distinct gene features including transcripts of greater length and exon number relative to unoccupied transcripts. H4K20me3- and H3K4me3-marked chromatin is also associated with processed RNAs (exon transcripts) relative to unspliced pre-mRNA and ncRNA transcripts. In summary, our results provide evidence that H4K20me3- and H3K4me3-associated RNAs represent a distinct subnetwork of the ES cell transcriptional repertoire.
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Affiliation(s)
- Jiji T Kurup
- From the Department of Oncology and.,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Benjamin L Kidder
- From the Department of Oncology and .,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
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15
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He R, Kidder BL. Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape. Sci Rep 2018; 8:10775. [PMID: 30018329 PMCID: PMC6050317 DOI: 10.1038/s41598-018-29074-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 01/07/2023] Open
Abstract
Pluripotent stem cells within the inner cell mass and epiblast of mammalian embryos have the capacity to form all lineages in the adult organism, while multipotent trophoblast stem (TS) cells derived from the trophectoderm are capable of differentiating into fetal lineages of the placenta. While mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) exhibit distinct expression patterns and utilize distinct external signaling pathways for self-renewal, because mouse EpiSCs resemble human ES cells they are a useful model to investigate mechanisms of human ES cell self-renewal and differentiation. Recent studies have shown that haploid embryos and ES cells can be generated from chemically-activated unfertilized mouse oocytes. However, it is unclear whether EpiSCs or TS cells can be derived from haploid embryos. Here, we describe the derivation of EpiSCs from haploid blastocyst-stage embryos using culture conditions that promote TS cell self-renewal. Maternal (parthenogenetic/gynogenetic) EpiSCs (maEpiSCs) functionally and morphologically resemble conventional EpiSCs. Established maEpiSCs and conventional EpiSCs are diploid and exhibit a normal number of chromosomes. Moreover, global expression analyses and epigenomic profiling revealed that maEpiSCs and conventional EpiSCs exhibit similarly primed transcriptional programs and epigenetic profiles, respectively. Altogether, our results describe a useful experimental model to generate EpiSCs from haploid embryos, provide insight into self-renewal mechanisms of EpiSCs, and suggest that FGF4 is not sufficient to derive TS cells from haploid blastocyst-stage embryos.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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16
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Xu J, Kidder BL. H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells. BMC Genomics 2018; 19:514. [PMID: 29969988 PMCID: PMC6029396 DOI: 10.1186/s12864-018-4886-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/19/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells. RESULTS Here, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements. CONCLUSIONS Overall, these findings highlight a previously undescribed subnetwork of ES cell transcriptional circuitry that utilizes dual marking of the repressive H4K20me3 mark with activating histone modifications.
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Affiliation(s)
- Jian Xu
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
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17
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Kidder BL. CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells. J Vis Exp 2018. [PMID: 29889205 DOI: 10.3791/57481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem (ES) cell self-renewal and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, epigenetic regulators, and post-translation modifications of histones that combinatorially influence the gene expression state of nearby genes. RNA has also been shown to interact with various proteins to regulate chromatin dynamics and gene expression. Chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) is a novel method to survey RNAs associated with chromatin proteins, while chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is a powerful genomics technique to map the location of post-translational modification of histones, transcription factors, and epigenetic modifiers on a global-scale in ES cells. Here, we describe methods to perform CARIP-Seq and ChIP-Seq, including library construction for next-generation sequencing, to generate global chromatin-associated RNA and epigenomic maps in ES cells.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine; Karmanos Cancer Institute, Wayne State University School of Medicine;
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18
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Abstract
Trophoblast stem (TS) cells derived from the trophectoderm (TE) of mammalian embryos have the ability to self-renew indefinitely or differentiate into fetal lineages of the placenta. Epigenetic control of gene expression plays an instrumental role in dictating the fate of TS cell self-renewal and differentiation. However, the roles of histone demethylases and activating histone modifications such as methylation of histone 3 lysine 4 (H3K4me3/me2) in regulating TS cell expression programs, and in priming the epigenetic landscape for trophoblast differentiation, are largely unknown. Here, we demonstrate that the H3K4 demethylase, KDM5B, regulates the H3K4 methylome and expression landscapes of TS cells. Depletion of KDM5B resulted in downregulation of TS cell self-renewal genes and upregulation of trophoblast-lineage genes, which was accompanied by altered H3K4 methylation. Moreover, we found that KDM5B resets the H3K4 methylation landscape during differentiation in the absence of the external self-renewal signal, FGF4, by removing H3K4 methylation from promoters of self-renewal genes, and of genes whose expression is enriched in TS cells. Altogether, our data indicate an epigenetic role for KDM5B in regulating H3K4 methylation in TS cells and during trophoblast differentiation. Summary: The histone 3 lysine 4 demethylase KDM5B plays a key role in regulating H3K4 methylation during trophoblast stem cell self-renewal and differentiation. KDM5B regulates the transcriptional profile of TS cells during self-renewal and differentiation, and resets the H3K4 methylation landscape during differentiation by removing H3K4me3 from promoters of self-renewal and TS cell enriched genes.
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Affiliation(s)
- Jian Xu
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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19
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He R, Kidder BL. H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells. Nucleic Acids Res 2017; 45:6427-6441. [PMID: 28402433 PMCID: PMC5499819 DOI: 10.1093/nar/gkx251] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 02/04/2023] Open
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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20
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He R, Xhabija B, Al-Qanber B, Kidder BL. OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells. Sci Rep 2017; 7:16360. [PMID: 29180818 PMCID: PMC5703885 DOI: 10.1038/s41598-017-16611-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022] Open
Abstract
Embryonic stem (ES) cell pluripotency is governed by OCT4-centric transcriptional networks. Conventional ES cells can be derived and maintained in vitro with media containing the cytokine leukemia inhibitory factor (LIF), which propagates the pluripotent state by activating STAT3 signaling, and simultaneous inhibition of glycogen synthase kinase-3 (GSK3) and MAP kinase/ERK kinase signaling. However, it is unclear whether overexpression of OCT4 is sufficient to overcome LIF-dependence. Here, we show that inducible expression of OCT4 (iOCT4) supports long-term LIF-independent self-renewal of ES cells cultured in media containing fetal bovine serum (FBS) and a glycogen synthase kinase-3 (GSK3) inhibitor, and in serum-free media. Global expression analysis revealed that LIF-independent iOCT4 ES cells and control ES cells exhibit similar transcriptional programs relative to epiblast stem cells (EpiSCs) and differentiated cells. Epigenomic profiling also demonstrated similar patterns of histone modifications between LIF-independent iOCT4 and control ES cells. Moreover, LIF-independent iOCT4 ES cells retain the capacity to differentiate in vitro and in vivo upon downregulation of OCT4 expression. These findings indicate that OCT4 expression is sufficient to sustain intrinsic signaling in a LIF-independent manner to promote ES cell pluripotency and self-renewal.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, MI, USA
| | - Batool Al-Qanber
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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21
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Kidder BL, He R, Wangsa D, Padilla-Nash HM, Bernardo MM, Sheng S, Ried T, Zhao K. SMYD5 Controls Heterochromatin and Chromosome Integrity during Embryonic Stem Cell Differentiation. Cancer Res 2017; 77:6729-6745. [PMID: 28951459 DOI: 10.1158/0008-5472.can-17-0828] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/10/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Epigenetic regulation of chromatin states is thought to control gene expression programs during lineage specification. However, the roles of repressive histone modifications, such as trimethylated histone lysine 20 (H4K20me3), in development and genome stability are largely unknown. Here, we show that depletion of SET and MYND domain-containing protein 5 (SMYD5), which mediates H4K20me3, leads to genome-wide decreases in H4K20me3 and H3K9me3 levels and derepression of endogenous LTR- and LINE-repetitive DNA elements during differentiation of mouse embryonic stem cells. SMYD5 depletion resulted in chromosomal aberrations and the formation of transformed cells that exhibited decreased H4K20me3 and H3K9me3 levels and an expression signature consistent with multiple human cancers. Moreover, dysregulated gene expression in SMYD5 cancer cells was associated with LTR and endogenous retrovirus elements and decreased H4K20me3. In addition, depletion of SMYD5 in human colon and lung cancer cells results in increased tumor growth and upregulation of genes overexpressed in colon and lung cancers, respectively. These findings implicate an important role for SMYD5 in maintaining chromosome integrity by regulating heterochromatin and repressing endogenous repetitive DNA elements during differentiation. Cancer Res; 77(23); 6729-45. ©2017 AACR.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan. .,Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Darawalee Wangsa
- Cancer Genomics Section, National Cancer Institute, NIH, Bethesda, Maryland
| | | | - M Margarida Bernardo
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan.,Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
| | - Shijie Sheng
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan.,Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
| | - Thomas Ried
- Cancer Genomics Section, National Cancer Institute, NIH, Bethesda, Maryland
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland.
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22
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Kidder BL, Hu G, Cui K, Zhao K. SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics Chromatin 2017; 10:8. [PMID: 28250819 PMCID: PMC5324308 DOI: 10.1186/s13072-017-0115-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/14/2017] [Indexed: 12/27/2022] Open
Abstract
Background Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone 4 lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Results Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation. SMYD5-bound regions are enriched with repetitive DNA elements. Knockdown of SMYD5 results in a global decrease of H4K20me3 levels, a redistribution of heterochromatin constituents including H3K9me3/2, G9a, and HP1α, and de-repression of endogenous retroelements. A loss of SMYD5-dependent silencing of heterochromatin nearby genic regions leads to upregulated expression of lineage-specific genes, thus contributing to the decreased self-renewal and perturbed differentiation of SMYD5-depleted ES cells. Conclusions Altogether, these findings implicate a role for SMYD5 in regulating ES cell self-renewal and H4K20me3-marked heterochromatin. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0115-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA.,Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
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Rosati R, Patki M, Chari V, Dakshnamurthy S, McFall T, Saxton J, Kidder BL, Shaw PE, Ratnam M. The Amino-terminal Domain of the Androgen Receptor Co-opts Extracellular Signal-regulated Kinase (ERK) Docking Sites in ELK1 Protein to Induce Sustained Gene Activation That Supports Prostate Cancer Cell Growth. J Biol Chem 2016; 291:25983-25998. [PMID: 27793987 PMCID: PMC5207070 DOI: 10.1074/jbc.m116.745596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/17/2016] [Indexed: 11/24/2022] Open
Abstract
The ETS domain transcription factor ELK1 is in a repressive association with growth genes and is transiently activated through phosphorylation by ERK1/2. In prostate cancer (PCa) cells the androgen receptor (AR) is recruited by ELK1, via its amino-terminal domain (A/B), as a transcriptional co-activator, without ELK1 hyper-phosphorylation. Here we elucidate the structural basis of the interaction of AR with ELK1. The ELK1 polypeptide motifs required for co-activation by AR versus those required for activation of ELK1 by ERK were systematically mapped using a mammalian two-hybrid system and confirmed using a co-immunoprecipitation assay. The mapping precisely identified the two ERK-docking sites in ELK1, the D-box and the DEF (docking site for ERK, FXFP) motif, as the essential motifs for its cooperation with AR(A/B) or WTAR. In contrast, the transactivation domain in ELK1 was only required for activation by ERK. ELK1-mediated transcriptional activity of AR(A/B) was optimal in the absence of ELK1 binding partners, ERK1/2 and serum-response factor. Purified ELK1 and AR bound with a dissociation constant of 1.9 × 10−8m. A purified mutant ELK1 in which the D-box and DEF motifs were disrupted did not bind AR. An ELK1 mutant with deletion of the D-box region had a dominant-negative effect on androgen-dependent growth of PCa cells that were insensitive to MEK inhibition. This novel mechanism in which a nuclear receptor impinges on a signaling pathway by co-opting protein kinase docking sites to constitutively activate growth genes could enable rational design of a new class of targeted drug interventions.
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Affiliation(s)
- Rayna Rosati
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology.,Wayne State University School of Medicine, Detroit, Michigan 48201-2013 and
| | - Mugdha Patki
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology.,Wayne State University School of Medicine, Detroit, Michigan 48201-2013 and
| | - Venkatesh Chari
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology
| | | | - Thomas McFall
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology.,Wayne State University School of Medicine, Detroit, Michigan 48201-2013 and
| | - Janice Saxton
- the School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Benjamin L Kidder
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology.,Wayne State University School of Medicine, Detroit, Michigan 48201-2013 and
| | - Peter E Shaw
- the School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Manohar Ratnam
- From the Barbara Ann Karmanos Cancer Institute and Department of Oncology, .,Wayne State University School of Medicine, Detroit, Michigan 48201-2013 and
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Abstract
Generation of induced pluripotent stem (iPS) cells from differentiated cells has traditionally been performed by overexpressing four transcription factors: Oct4, Sox2, Klf4, and c-Myc. However, inclusion of c-Myc in the reprogramming cocktail can lead to expansion of transformed cells that are not fully reprogrammed, and studies have demonstrated that c-Myc reactivation increases tumorigenicity in chimeras and progeny mice. Moreover, chemical inhibition of Wnt signaling has been shown to enhance reprogramming efficiency. Here, we describe a modified protocol for generating iPS cells from murine fibroblasts using chemical inhibition and overexpression of three transcription factors. Using this protocol, we observed robust conversion to iPS cells while maintaining minimal contamination of partially reprogrammed transformed colonies.
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Affiliation(s)
- Benjamin L Kidder
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 10, Room 7B04, 10 Center Drive, Bethesda, MD, 20892, USA,
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25
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Abstract
The trophoblast is the first lineage to undergo differentiation during mammalian development. In the preimplantation blastocyst embryo, two cell types are present including the inner cell mass (ICM) and the trophectoderm (TE). ICM cells exhibit pluripotent potential, or the capacity to give rise to all cells represented in the adult organism, while TE cells are multipotent and are therefore only capable of differentiating into trophoblast lineages represented in the placenta. The TE is essential for implantation of the embryo into the uterine tissue, formation of trophoblast lineages represented in the placenta, and exchange of nutrients and waste between the embryo and the mother. Trophoblast stem (TS) cells, which can be derived from the TE of preimplantation embryos in the presence of external signals such as FGF4, can self-renew indefinitely, and because they are capable of differentiating into epithelial lineages of the trophoblast, TS cells are a useful in vitro model to study the biology of the trophoblast including epigenetic regulation of gene expression. In this chapter we describe protocols for derivation of TS cells from mouse blastocysts, culture conditions that promote self-renewal and differentiation, and methods to transduce TS cells with lentiviral particles encoding shRNAs. These protocols are sufficient for efficient derivation of TS cells and robust RNAi knockdown of target genes in TS cells.
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Affiliation(s)
- Benjamin L Kidder
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Dr., Bldg 10, 7B04, Bethesda, MD, 20892, USA,
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Kidder BL, Hu G, Zhao K. KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. Genome Biol 2014; 15:R32. [PMID: 24495580 PMCID: PMC4053761 DOI: 10.1186/gb-2014-15-2-r32] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/04/2014] [Indexed: 01/07/2023] Open
Abstract
Background Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Results Here, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes. Conclusions Our results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.
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Kidder BL, Zhao K. Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells. Methods Mol Biol 2014; 1150:3-20. [PMID: 24743988 DOI: 10.1007/978-1-4939-0512-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Gene expression in embryonic stem (ES) cells is regulated in part by a network of transcription factors, epigenetic regulators, and histone modifications that influence the underlying chromatin in a way that is conducive or repressive for transcription. Advances in next-generation sequencing technology have allowed for the genome-wide analysis of chromatin constituents and protein-DNA interactions at high resolution in ES cells and other stem cells. While many studies have surveyed genome-wide profiles of a few factors and expression changes at a fixed time point in undifferentiated ES cells, few have utilized an integrative approach to simultaneously survey protein-DNA interactions, histone modifications, and expression programs during ES cell self-renewal and differentiation. To identify transcriptional networks that regulate pluripotency and differentiation, it is important to generate high-quality genome-wide maps of transcription factors, chromatin factors, and histone modifications and to survey global gene expression profiles. Here, to interrogate genome-wide profiles of chromatin features and to survey global gene expression programs in ES cells, we describe protocols for efficient library construction for next-generation sequencing of ChIP-Seq and RNA-Seq samples.
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Affiliation(s)
- Benjamin L Kidder
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Dr., Bldg 10, 7B04, Bethesda, MD, 20892, USA,
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Abstract
Epigenetic regulation of gene expression is important in maintaining self-renewal of embryonic stem (ES) and trophoblast stem (TS) cells. Histone deacetylases (HDACs) negatively control histone acetylation by removing covalent acetylation marks from histone tails. Because histone acetylation is a known mark for active transcription, HDACs presumably associate with inactive genes. Here, we used genome-wide chromatin immunoprecipitation to investigate targets of HDAC1 in ES and TS cells. Through evaluation of genes associated with acetylated histone H3 marks, and global expression analysis of Hdac1 knockout ES and trichostatin A-treated ES and TS cells, we found that HDAC1 occupies mainly active genes, including important regulators of ES and TS cells self-renewal. We also observed occupancy of methyl-CpG binding domain protein 3 (MBD3), a subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex, at a subset of HDAC1-occupied sequences in ES cells, including the pluripotency regulators Oct4, Nanog and Kfl4. By mapping HDAC1 targets on a global scale, our results describe further insight into epigenetic mechanisms of ES and TS cells self-renewal.
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Kidder BL, Palmer S. Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance. Genome Res 2010; 20:458-72. [PMID: 20176728 DOI: 10.1101/gr.101469.109] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (FGF4, INHBA/NODAL/TGFB1) for self-renewal. While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells, we used chromatin immunoprecipitation with DNA microarray hybridization (ChIP-chip) analysis to investigate targets of the TFs-TCFAP2C, EOMES, ETS2, and GATA3-and a chromatin remodeling factor, SMARCA4. We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (AcH3). Our results describe previously unknown transcriptional networks in TS cells, including TF occupancy of genes involved in ES cell self-renewal and pluripotency, co-occupancy of TCFAP2C, SMARCA4, and EOMES at a significant number of genes, and transcriptional regulatory circuitry within the five factors. Moreover, RNAi depletion of Tcfap2c, Smarca4, and Eomes transcripts resulted in a loss of normal colony morphology and down-regulation of TS cell-specific genes, suggesting an important role for TCFAP2C, SMARCA4, and EOMES in TS cell self-renewal. Through genome-wide mapping and global expression analysis of five TF target genes, our data provide a comprehensive analysis of transcriptional networks that regulate TS cell self-renewal.
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Abstract
The SWI/SNF-Brg1 chromatin remodeling protein plays critical roles in cell-cycle control and differentiation through regulation of gene expression. Loss of Brg1 in mice results in early embryonic lethality, and recent studies have implicated a role for Brg1 in somatic stem cell self-renewal and differentiation. However, little is known about Brg1 function in preimplantation embryos and embryonic stem (ES) cells. Here we report that Brg1 is required for ES cell self-renewal and pluripotency. RNA interference-mediated knockdown of Brg1 in blastocysts caused aberrant expression of Oct4 and Nanog. In ES cells, knockdown of Brg1 resulted in phenotypic changes indicative of differentiation, downregulation of self-renewal and pluripotency genes (e.g., Oct4, Sox2, Sall4, Rest), and upregulation of differentiation genes. Using genome-wide promoter analysis (chromatin immunoprecipitation) we found that Brg1 occupied the promoters of key pluripotency-related genes, including Oct4, Sox2, Nanog, Sall4, Rest, and Polycomb group (PcG) proteins. Moreover, Brg1 co-occupied a subset of Oct4, Sox2, Nanog, and PcG protein target genes. These results demonstrate an important role for Brg1 in regulating self-renewal and pluripotency in ES cells.
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Kidder BL, Oseth L, Miller S, Hirsch B, Verfaillie C, Coucouvanis E. Embryonic stem cells contribute to mouse chimeras in the absence of detectable cell fusion. Cloning Stem Cells 2008; 10:231-48. [PMID: 18338954 DOI: 10.1089/clo.2007.0039] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Embryonic stem (ES) cells are capable of differentiating into all embryonic and adult cell types following mouse chimera production. Although injection of diploid ES cells into tetraploid blastocysts suggests that tetraploid cells have a selective disadvantage in the developing embryo, tetraploid hybrid cells, formed by cell fusion between ES cells and somatic cells, have been reported to contribute to mouse chimeras. In addition, other examples of apparent stem cell plasticity have recently been shown to be the result of cell fusion. Here we investigate whether ES cells contribute to mouse chimeras through a cell fusion mechanism. Fluorescence in situ hybridization (FISH) analysis for X and Y chromosomes was performed on dissociated tissues from embryonic, neonatal, and adult wild-type, and chimeric mice to follow the ploidy distributions of cells from various tissues. FISH analysis showed that the ploidy distributions in dissociated tissues, notably the tetraploid cell number, did not differ between chimeric and wild-type tissues. To address the possibility that early cell fusion events are hidden by subsequent reductive divisions or other changes in cell ploidy, we injected Z/EG (lacZ/EGFP) ES cells into ACTB-cre blastocysts. Recombination can only occur as the result of cell fusion, and the recombined allele should persist through any subsequent changes in cell ploidy. We did not detect evidence of fusion in embryonic chimeras either by direct fluorescence microscopy for GFP or by PCR amplification of the recombined Z/EG locus on genomic DNA from ACTB-cre::Z/EG chimeric embryos. Our results argue strongly against cell fusion as a mechanism by which ES cells contribute to chimeras.
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Affiliation(s)
- Benjamin L Kidder
- Department of Medicine, Stem Cell Institute, Minneapolis, Minnesota, USA
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Kidder BL, de Matos D, Knott JG, Palmer S. Identifying Markers of Embryo Quality: Brg1 Regulates Transcriptional Activation of Stat3 Target Genes in ES Cells and Preimplantation Embryos. Biol Reprod 2008. [DOI: 10.1093/biolreprod/78.s1.85b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ulloa-Montoya F, Kidder BL, Pauwelyn KA, Chase LG, Luttun A, Crabbe A, Geraerts M, Sharov AA, Piao Y, Ko MSH, Hu WS, Verfaillie CM. Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. Genome Biol 2008; 8:R163. [PMID: 17683608 PMCID: PMC2374994 DOI: 10.1186/gb-2007-8-8-r163] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/04/2007] [Accepted: 08/06/2007] [Indexed: 01/22/2023] Open
Abstract
Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells. Background Recently, several populations of postnatal stem cells, such as multipotent adult progenitor cells (MAPCs), have been described that have broader differentiation ability than classical adult stem cells. Here we compare the transcriptome of pluripotent embryonic stem cells (ESCs), MAPCs, and lineage-restricted mesenchymal stem cells (MSCs) to determine their relationship. Results Applying principal component analysis, non-negative matrix factorization and k-means clustering algorithms to the gene-expression data, we identified a unique gene-expression profile for MAPCs. Apart from the ESC-specific transcription factor Oct4 and other ESC transcripts, some of them associated with maintaining ESC pluripotency, MAPCs also express transcripts characteristic of early endoderm and mesoderm. MAPCs do not, however, express Nanog or Sox2, two other key transcription factors involved in maintaining ESC properties. This unique molecular signature was seen irrespective of the microarray platform used and was very similar for both mouse and rat MAPCs. As MSC-like cells isolated under MAPC conditions are virtually identical to MSCs, and MSCs cultured in MAPC conditions do not upregulate MAPC-expressed transcripts, the MAPC signature is cell-type specific and not merely the result of differing culture conditions. Conclusion Multivariate analysis techniques clustered stem cells on the basis of their expressed gene profile, and the genes determining this clustering reflected the stem cells' differentiation potential in vitro. This comparative transcriptome analysis should significantly aid the isolation and culture of MAPCs and MAPC-like cells, and form the basis for studies to gain insights into genes that confer on these cells their greater developmental potency.
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Affiliation(s)
- Fernando Ulloa-Montoya
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Benjamin L Kidder
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen A Pauwelyn
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Lucas G Chase
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aernout Luttun
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Annelies Crabbe
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Martine Geraerts
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Alexei A Sharov
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Minoru SH Ko
- Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Catherine M Verfaillie
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium
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Chase LG, Ulloa-Montoya F, Kidder BL, Verfaillie CM. Islet-derived fibroblast-like cells are not derived via epithelial-mesenchymal transition from Pdx-1 or insulin-positive cells. Diabetes 2007; 56:3-7. [PMID: 17110468 DOI: 10.2337/db06-1165] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As recent studies suggest that newly formed pancreatic beta-cells are a result of self-duplication rather than stem cell differentiation, in vitro expansion of beta-cells presents a potential mechanism by which to increase available donor tissue for cell-based diabetes therapies. Although most studies have found that beta-cells are resilient to substantial in vitro expansion, recent studies have suggested that it is possible to expand these cells through a process referred to as epithelial-mesenchymal transition (EMT). To further substantiate such an expansion mechanism, we used recombination-based genetic lineage tracing to determine the origin of proliferating fibroblast-like cells from cultured pancreatic islets in vitro. We demonstrate, using two culture methods, that EMT does not underlie the appearance of fibroblast-like cells in mouse islet cultures but that fibroblast-like cells appear to represent mesenchymal stem cell (MSC)-like cells akin to MSCs isolated from bone marrow.
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Affiliation(s)
- Lucas G Chase
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
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35
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Hoffman MP, Kidder BL, Steinberg ZL, Lakhani S, Ho S, Kleinman HK, Larsen M. Gene expression profiles of mouse submandibular gland development: FGFR1 regulates branching morphogenesis in vitro through BMP- and FGF-dependent mechanisms. Development 2002; 129:5767-78. [PMID: 12421715 DOI: 10.1242/dev.00172] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analyses of gene expression profiles at five different stages of mouse submandibular salivary gland development provide insight into gland organogenesis and identify genes that may be critical at different stages. Genes with similar expression profiles were clustered, and RT-PCR was used to confirm the developmental changes. We focused on fibroblast growth factor receptor 1 (FGFR1), as its expression is highest early in gland development. We extended our array results and analyzed the developmental expression patterns of other FGFR and FGF isoforms. The functional significance of FGFR1 was confirmed by submandibular gland organ culture. Antisense oligonucleotides decreased expression of FGFR1 and reduced branching morphogenesis of the glands. Inhibiting FGFR1 signaling with SU5402, a FGFR1 tyrosine kinase inhibitor, reduced branching morphogenesis. SU5402 treatment decreased cell proliferation but did not increase apoptosis. Fgfr, Fgf and Bmp gene expression was localized to either the mesenchyme or the epithelium by PCR, and then measured over time by real time PCR after SU5402 treatment. FGFR1 signaling regulates Fgfr1, Fgf1, Fgf3 and Bmp7 expression and indirectly regulates Fgf7, Fgf10 and Bmp4. Exogenous FGFs and BMPs added to glands in culture reveal distinct effects on gland morphology. Glands cultured with SU5402 were then rescued with exogenous BMP7, FGF7 or FGF10. Taken together, our results suggest specific FGFs and BMPs play reciprocal roles in regulating branching morphogenesis and FGFR1 signaling plays a central role by regulating both FGF and BMP expression.
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Affiliation(s)
- Matthew P Hoffman
- Craniofacial Developmental Biology and Regeneration Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, MSC 4370, Bethesda, MD 20892-4370, USA.
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