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Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency. Cell Stem Cell 2020; 27:459-469.e8. [PMID: 32795400 DOI: 10.1016/j.stem.2020.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 02/07/2020] [Accepted: 07/02/2020] [Indexed: 12/23/2022]
Abstract
Mouse embryonic stem cells (mESCs) cultured in the presence of LIF occupy a ground state with highly active pluripotency-associated transcriptional and epigenetic circuitry. However, ground state pluripotency in some inbred strain backgrounds is unstable in the absence of ERK1/2 and GSK3 inhibition. Using an unbiased genetic approach, we dissect the basis of this divergent response to extracellular cues by profiling gene expression and chromatin accessibility in 170 genetically heterogeneous mESCs. We map thousands of loci affecting chromatin accessibility and/or transcript abundance, including 10 QTL hotspots where genetic variation at a single locus coordinates the regulation of genes throughout the genome. For one hotspot, we identify a single enhancer variant ∼10 kb upstream of Lifr associated with chromatin accessibility and mediating a cascade of molecular events affecting pluripotency. We validate causation through reciprocal allele swaps, demonstrating the functional consequences of noncoding variation in gene regulatory networks that stabilize pluripotent states in vitro.
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Garg V, Morgani S, Hadjantonakis AK. Capturing Identity and Fate Ex Vivo: Stem Cells from the Mouse Blastocyst. Curr Top Dev Biol 2016; 120:361-400. [PMID: 27475857 DOI: 10.1016/bs.ctdb.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During mouse preimplantation development, three molecularly, morphologically, and spatially distinct lineages are formed, the embryonic epiblast, the extraembryonic primitive endoderm, and the trophectoderm. Stem cell lines representing each of these lineages have now been derived and can be indefinitely maintained and expanded in culture, providing an unlimited source of material to study the interplay of tissue-specific transcription factors and signaling pathways involved in these fundamental cell fate decisions. Here we outline our current understanding of the derivation, maintenance, and properties of these in vitro stem cell models representing the preimplantation embryonic lineages.
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Affiliation(s)
- V Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States
| | - S Morgani
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States.
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Huijbers IJ, Del Bravo J, Bin Ali R, Pritchard C, Braumuller TM, van Miltenburg MH, Henneman L, Michalak EM, Berns A, Jonkers J. Using the GEMM-ESC strategy to study gene function in mouse models. Nat Protoc 2015; 10:1755-85. [PMID: 26492136 DOI: 10.1038/nprot.2015.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Preclinical in vivo validation of target genes for therapeutic intervention requires careful selection and characterization of the most suitable animal model in order to assess the role of these genes in a particular process or disease. To this end, genetically engineered mouse models (GEMMs) are typically used. However, the appropriate engineering of these models is often cumbersome and time consuming. Recently, we and others described a modular approach for fast-track modification of existing GEMMs by re-derivation of embryonic stem cells (ESCs) that can be modified by recombinase-mediated transgene insertion and subsequently used for the production of chimeric mice. This 'GEMM-ESC strategy' allows for rapid in vivo analysis of gene function in the chimeras and their offspring. Moreover, this strategy is compatible with CRISPR/Cas9-mediated genome editing. This protocol describes when and how to use the GEMM-ESC strategy effectively, and it provides a detailed procedure for re-deriving and manipulating GEMM-ESCs under feeder- and serum-free conditions. This strategy produces transgenic mice with the desired complex genotype faster than traditional methods: generation of validated GEMM-ESC clones for controlled transgene integration takes 9-12 months, and recombinase-mediated transgene integration and chimeric cohort production takes 2-3 months. The protocol requires skills in embryology, stem cell biology and molecular biology, and it is ideally performed within, or in close collaboration with, a transgenic facility.
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Affiliation(s)
- Ivo J Huijbers
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jessica Del Bravo
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rahmen Bin Ali
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Colin Pritchard
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tanya M Braumuller
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Linda Henneman
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ewa M Michalak
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anton Berns
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Skoltech Center for Stem Cell Research, Moscow Region, Russia
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Howell GR, MacNicoll KH, Braine CE, Soto I, Macalinao DG, Sousa GL, John SWM. Combinatorial targeting of early pathways profoundly inhibits neurodegeneration in a mouse model of glaucoma. Neurobiol Dis 2014; 71:44-52. [PMID: 25132557 DOI: 10.1016/j.nbd.2014.07.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/27/2014] [Accepted: 07/16/2014] [Indexed: 12/18/2022] Open
Abstract
The endothelin system is implicated in various human and animal glaucomas. Targeting the endothelin system has great promise as a treatment for human glaucoma, but the cell types involved and the exact mechanisms of action are not clearly elucidated. Here, we report a detailed characterization of the endothelin system in specific cell types of the optic nerve head (ONH) during glaucoma in DBA/2J mice. First, we show that key components of the endothelin system are expressed in multiple cell types. We discover that endothelin 2 (EDN2) is expressed in astrocytes as well as microglia/monocytes in the ONH. The endothelin receptor type A (Ednra) is expressed in vascular endothelial cells, while the endothelin receptor type B (Ednrb) receptor is expressed in ONH astrocytes. Second, we show that Macitentan treatment protects from glaucoma. Macitentan is a novel, orally administered, dual endothelin receptor antagonist with greater affinity, efficacy and safety than previous antagonists. Finally, we test the combinatorial effect of targeting both the endothelin and complement systems as a treatment for glaucoma. Similar to endothelin, the complement system is implicated in a variety of human and animal glaucomas, and has great promise as a treatment target. We discovered that combined targeting of the endothelin (Bosentan) and complement (C1qa mutation) systems is profoundly protective. Remarkably, 80% of DBA/2J eyes subjected to this combined inhibition developed no detectable glaucoma. This opens an exciting new avenue for neuroprotection in glaucoma.
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Affiliation(s)
- Gareth R Howell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA.
| | | | | | - Ileana Soto
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | | | - Gregory L Sousa
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Simon W M John
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA; The Howard Hughes Medical Institute, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA; Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA.
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Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains. Nat Protoc 2014; 9:559-74. [PMID: 24504480 DOI: 10.1038/nprot.2014.030] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mouse embryonic stem cells (mESCs) are key tools for genetic engineering, development of stem cell-based therapies and basic research on pluripotency and early lineage commitment. However, successful derivation of germline-competent embryonic stem cell lines has, until recently, been limited to a small number of inbred mouse strains. Recently, there have been considerable advances in the field of embryonic stem cell biology, particularly in the area of pluripotency maintenance in the epiblast from which the mESCs are derived. Here we describe a protocol for efficient derivation of germline-competent mESCs from any mouse strain, including strains previously deemed nonpermissive. We provide a protocol that is generally applicable to most inbred strains, as well as a variant for nonpermissive strains. By using this protocol, mESCs can be derived in 3 weeks and fully characterized after an additional 12 weeks, at efficiencies as high as 90% and in any strain background.
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Huijbers IJ, Bin Ali R, Pritchard C, Cozijnsen M, Kwon MC, Proost N, Song JY, de Vries H, Badhai J, Sutherland K, Krimpenfort P, Michalak EM, Jonkers J, Berns A. Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells. EMBO Mol Med 2014; 6:212-25. [PMID: 24401838 PMCID: PMC3927956 DOI: 10.1002/emmm.201303297] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Human cancers modeled in Genetically Engineered Mouse Models (GEMMs) can provide important mechanistic insights into the molecular basis of tumor development and enable testing of new intervention strategies. The inherent complexity of these models, with often multiple modified tumor suppressor genes and oncogenes, has hampered their use as preclinical models for validating cancer genes and drug targets. In our newly developed approach for the fast generation of tumor cohorts we have overcome this obstacle, as exemplified for three GEMMs; two lung cancer models and one mesothelioma model. Three elements are central for this system; (i) The efficient derivation of authentic Embryonic Stem Cells (ESCs) from established GEMMs, (ii) the routine introduction of transgenes of choice in these GEMM-ESCs by Flp recombinase-mediated integration and (iii) the direct use of the chimeric animals in tumor cohorts. By applying stringent quality controls, the GEMM-ESC approach proofs to be a reliable and effective method to speed up cancer gene assessment and target validation. As proof-of-principle, we demonstrate that MycL1 is a key driver gene in Small Cell Lung Cancer.
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Affiliation(s)
- Ivo J Huijbers
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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