1
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Huang S, Henderson TR, Dojo Soeandy C, Lezhanska A, Henderson JT. An efficient low cost means of biophysical gene transfection in primary cells. Sci Rep 2024; 14:13179. [PMID: 38849388 PMCID: PMC11161637 DOI: 10.1038/s41598-024-62996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Efficient, facile gene modification of cells has become an indispensable part of modern molecular biology. For the majority of cell lines and several primary populations, such modifications can be readily performed through a variety of methods. However, many primary cell lines such as stem cells frequently suffer from poor transfection efficiency. Though several physical approaches have been introduced to circumvent these issues, they often require expensive/specialized equipment and/or consumables, utilize substantial cell numbers and often still suffer from poor efficiency. Viral methods are capable of transducing difficult cellular populations, however such methods can be time consuming for large arrays of gene targets, present biohazard concerns, and result in expression of viral proteins; issues of concern for certain experimental approaches. We report here a widely applicable, low-cost (< $100 CAD) method of electroporation, applicable to small (1-10 μl) cell volumes and composed of equipment readily available to the average investigator. Using this system we observe a sixfold increase in transfection efficiency in embryonic stem cell lines compared to commercial devices. Due to efficiency gains and reductions in volume and applied voltage, this process improves the survival of sensitive stem cell populations while reducing reagent requirements for protocols such as Cas9/gRNAs transfections.
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Affiliation(s)
- Shudi Huang
- Department of Pharmaceutical Sciences, University of Toronto, 144 College St. Rm 962, Toronto, ON, M5S 3M2, Canada
| | - Tyler R Henderson
- Department of Medical Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chesarahmia Dojo Soeandy
- Tumour Immunotherapy Program Cell Manufacturing Team, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Rm 8-207, Toronto, ON, M5G 2M9, Canada
| | - Anastasiya Lezhanska
- Department of Medicine, Queen's University, 94 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Jeffrey T Henderson
- Department of Pharmaceutical Sciences, University of Toronto, 144 College St. Rm 962, Toronto, ON, M5S 3M2, Canada.
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2
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Bansal P, Banda EC, Glatt-Deeley HR, Stoddard CE, Linsley JW, Arora N, Deleschaux C, Ahern DT, Kondaveeti Y, Massey RE, Nicouleau M, Wang S, Sabariego-Navarro M, Dierssen M, Finkbeiner S, Pinter SF. A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction. SCIENCE ADVANCES 2024; 10:eadj0385. [PMID: 38848354 PMCID: PMC11160455 DOI: 10.1126/sciadv.adj0385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. To address this question in a model of DS neurogenesis, we derived trisomy 21 (T21) human induced pluripotent stem cells (iPSCs) alongside, otherwise, isogenic euploid controls from mosaic DS fibroblasts and equipped one chr21 copy with an inducible XIST transgene. Monoallelic chr21 silencing by XIST is near-complete and irreversible in iPSCs. Differential expression reveals that T21 neural lineages and iPSCs share suppressed translation and mitochondrial pathways and activate cellular stress responses. When XIST is induced before the neural progenitor stage, T21 dosage correction suppresses a pronounced skew toward astrogenesis in neural differentiation. Because our transgene remains inducible in postmitotic T21 neurons and astrocytes, we demonstrate that XIST efficiently represses genes even after terminal differentiation, which will empower exploration of cell type-specific T21 phenotypes that remain responsive to chr21 dosage.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Christopher E. Stoddard
- Cell and Genome Engineering Core, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Jeremy W. Linsley
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Neha Arora
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Cécile Deleschaux
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Rachael E. Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Michael Nicouleau
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Shijie Wang
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Miguel Sabariego-Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Human Pharmacology and Clinical Neurosciences Research Group, Neurosciences Research Program, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA, USA
- Neuroscience and Biomedical Sciences Graduate Programs, University of California San Francisco, San Francisco, CA, USA
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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3
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Tomris I, van der Woude R, de Paiva Froes Rocha R, Torrents de la Peña A, Ward AB, de Vries RP. Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding. Protein Sci 2024; 33:e4974. [PMID: 38533540 DOI: 10.1002/pro.4974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
Enveloped viruses carry one or multiple proteins with receptor-binding functionalities. Functional receptors can be glycans, proteinaceous, or both; therefore, recombinant protein approaches are instrumental in attaining new insights regarding viral envelope protein receptor-binding properties. Visualizing and measuring receptor binding typically entails antibody detection or direct labeling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here, we report a suite of distinct fluorescent fusions, both N- and C-terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained three or six fluorescent protein barrels and were applied directly to cells to assess receptor binding properties.
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Affiliation(s)
- Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Rebeca de Paiva Froes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
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4
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Huang S, Suo NJ, Henderson TR, Macgregor RB, Henderson JT. Cellular transfection using rapid decrease in hydrostatic pressure. Sci Rep 2024; 14:4631. [PMID: 38409237 PMCID: PMC10897145 DOI: 10.1038/s41598-024-54463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Of all methods exercised in modern molecular biology, modification of cellular properties through the introduction or removal of nucleic acids is one of the most fundamental. As such, several methods have arisen to promote this process; these include the condensation of nucleic acids with calcium, polyethylenimine or modified lipids, electroporation, viral production, biolistics, and microinjection. An ideal transfection method would be (1) low cost, (2) exhibit high levels of biological safety, (3) offer improved efficacy over existing methods, (4) lack requirements for ongoing consumables, (5) work efficiently at any scale, (6) work efficiently on cells that are difficult to transfect by other methods, and (7) be capable of utilizing the widest array of existing genetic resources to facilitate its utility in research, biotechnical and clinical settings. To address such issues, we describe here Pressure-jump-poration (PJP), a method using rapid depressurization to transfect even difficult to modify primary cell types such as embryonic stem cells. The results demonstrate that PJP can be used to introduce an array of genetic modifiers in a safe, sterile manner. Finally, PJP-induced transfection in primary versus transformed cells reveals a surprising dichotomy between these classes which may provide further insight into the process of cellular transformation.
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Affiliation(s)
- Shudi Huang
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Nan Ji Suo
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Tyler R Henderson
- Department of Medical Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Jeffrey T Henderson
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada.
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5
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Abarinov V, Levine JA, Churchill AJ, Hopwood B, Deiter CS, Guney MA, Wells KL, Schrunk JM, Guo Y, Hammelman J, Gifford DK, Magnuson MA, Wichterle H, Sussel L. Major β cell-specific functions of NKX2.2 are mediated via the NK2-specific domain. Genes Dev 2023; 37:490-504. [PMID: 37364986 PMCID: PMC10393193 DOI: 10.1101/gad.350569.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023]
Abstract
The consolidation of unambiguous cell fate commitment relies on the ability of transcription factors (TFs) to exert tissue-specific regulation of complex genetic networks. However, the mechanisms by which TFs establish such precise control over gene expression have remained elusive-especially in instances in which a single TF operates in two or more discrete cellular systems. In this study, we demonstrate that β cell-specific functions of NKX2.2 are driven by the highly conserved NK2-specific domain (SD). Mutation of the endogenous NKX2.2 SD prevents the developmental progression of β cell precursors into mature, insulin-expressing β cells, resulting in overt neonatal diabetes. Within the adult β cell, the SD stimulates β cell performance through the activation and repression of a subset of NKX2.2-regulated transcripts critical for β cell function. These irregularities in β cell gene expression may be mediated via SD-contingent interactions with components of chromatin remodelers and the nuclear pore complex. However, in stark contrast to these pancreatic phenotypes, the SD is entirely dispensable for the development of NKX2.2-dependent cell types within the CNS. Together, these results reveal a previously undetermined mechanism through which NKX2.2 directs disparate transcriptional programs in the pancreas versus neuroepithelium.
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Affiliation(s)
- Vladimir Abarinov
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Joshua A Levine
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Angela J Churchill
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Bryce Hopwood
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Cailin S Deiter
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Michelle A Guney
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Kristen L Wells
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jessica M Schrunk
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Yuchun Guo
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jennifer Hammelman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
- Department of Neurology, Columbia University, New York, New York 10032, USA
- Department of Neuroscience, Columbia University, New York, New York 10032, USA
| | - Lori Sussel
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA;
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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6
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Biggs D, Chen CM, Davies B. Targeted Integration of Transgenes at the Mouse Gt(ROSA)26Sor Locus. Methods Mol Biol 2023; 2631:299-323. [PMID: 36995674 DOI: 10.1007/978-1-0716-2990-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The targeting of transgenic constructs at single copy into neutral genomic loci avoids the unpredictable outcomes associated with conventional random integration approaches. The Gt(ROSA)26Sor locus on chromosome 6 has been used many times for the integration of transgenic constructs and is known to be permissive for transgene expression and disruption of the gene is not associated with a known phenotype. Furthermore, the transcript made from the Gt(ROSA)26Sor locus is ubiquitously expressed and subsequently the locus can be used to drive the ubiquitous expression of transgenes.Here we report a protocol for the generation of targeted transgenic alleles at Gt(ROSA)26Sor, taking as an example a conditional overexpression allele, by PhiC31 integrase/recombinase-mediated cassette exchange of an engineered Gt(ROSA)26Sor locus in mouse embryonic stem cells. The overexpression allele is initially silenced by the presence of a loxP flanked stop sequence but can be strongly activated through the action of Cre recombinase.
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Affiliation(s)
- Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chiann-Mun Chen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- The Francis Crick Institute, London, UK.
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7
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Zheng D, Wang X, Zhang Z, Li E, Yeung C, Borkar R, Qin G, Wu Y, Xu RH. Engineering of human mesenchymal stem cells resistant to multiple natural killer subtypes. Int J Biol Sci 2022; 18:426-440. [PMID: 34975342 PMCID: PMC8692142 DOI: 10.7150/ijbs.64640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Mesenchymal stem cells (MSCs) as a therapeutic promise are often quickly cleared by innate immune cells of the host including natural killer (NK) cells. Efforts have been made to generate immune-escaping human embryonic stem cells (hESCs) where T cell immunity is evaded by defecting β-2-microglobulin (B2M), a common unit for human leukocyte antigen (HLA) class I, and NK cells are inhibited via ectopic expression of HLA-E or -G. However, NK subtypes vary among recipients and even at different pathologic statuses. It is necessary to dissect and optimize the efficacy of the immune-escaping cells against NK subtypes. Here, we first generated B2M knockout hESCs and differentiated them to MSCs (EMSCs) and found that NK resistance occurred with B2M-/- EMSCs expressing HLA-E and -G only when they were transduced via an inducible lentiviral system in a dose-dependent manner but not when they were inserted into a safe harbor. HLA-E and -G expressed at high levels together in transduced EMSCs inhibited three major NK subtypes, including NKG2A+/LILRB1+, NKG2A+/LILRB1-, and NKG2A-/LILRB1+, which was further potentiated by IFN-γ priming. Thus, this study engineers MSCs with resistance to multiple NK subtypes and underscores that dosage matters when a transgene is used to confer a novel effect to host cells, especially for therapeutic cells to evade immune rejection.
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Affiliation(s)
- Dejin Zheng
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Xiaoyan Wang
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Zhenwu Zhang
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Enqin Li
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Cheungkwan Yeung
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Roma Borkar
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Guihui Qin
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Yaojiong Wu
- The Shenzhen Key Laboratory of Health Sciences and Technology, International Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Ren-He Xu
- Center of Reproduction, Development & Aging, and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
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8
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Trotman JB, Lee DM, Cherney RE, Kim SO, Inoue K, Schertzer MD, Bischoff SR, Cowley DO, Calabrese J. Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity. Nucleic Acids Res 2020; 48:10500-10517. [PMID: 32986830 PMCID: PMC7544216 DOI: 10.1093/nar/gkaa789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 12/22/2022] Open
Abstract
The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of downstream polyadenylation sequences. Readthrough required Repeat A and the ∼750 nucleotides downstream, did not require SPEN, and was attenuated by splicing. Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcription, whereas a 5.5-kb Xist transgene robustly silenced transcription and read through its polyadenylation sequence. Longer, spliced Xist transgenes also induced robust silencing yet terminated efficiently. Thus, in contexts examined here, Xist requires sequence elements beyond its first two kilobases to robustly silence transcription, and the 5' end of Xist harbors SPEN-independent transcriptional antiterminator activity that can repress proximal cleavage and polyadenylation. In endogenous contexts, this antiterminator activity may help produce full-length Xist RNA while rendering the Xist locus resistant to silencing by the same repressive complexes that the lncRNA recruits to other genes.
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Affiliation(s)
- Jackson B Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Rachel E Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Susan O Kim
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Steven R Bischoff
- Animal Models Core, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Animal Models Core, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
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9
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Pericoli G, Petrini S, Giorda E, Ferretti R, Ajmone-Cat MA, Court W, Conti LA, De Simone R, Bencivenga P, Palma A, Di Giannatale A, Jones C, Carai A, Mastronuzzi A, de Billy E, Locatelli F, Vinci M. Integration of Multiple Platforms for the Analysis of Multifluorescent Marking Technology Applied to Pediatric GBM and DIPG. Int J Mol Sci 2020; 21:E6763. [PMID: 32942636 PMCID: PMC7555235 DOI: 10.3390/ijms21186763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 12/15/2022] Open
Abstract
The intratumor heterogeneity represents one of the most difficult challenges for the development of effective therapies to treat pediatric glioblastoma (pGBM) and diffuse intrinsic pontine glioma (DIPG). These brain tumors are composed of heterogeneous cell subpopulations that coexist and cooperate to build a functional network responsible for their aggressive phenotype. Understanding the cellular and molecular mechanisms sustaining such network will be crucial for the identification of new therapeutic strategies. To study more in-depth these mechanisms, we sought to apply the Multifluorescent Marking Technology. We generated multifluorescent pGBM and DIPG bulk cell lines randomly expressing six different fluorescent proteins and from which we derived stable optical barcoded single cell-derived clones. In this study, we focused on the application of the Multifluorescent Marking Technology in 2D and 3D in vitro/ex vivo culture systems. We discuss how we integrated different multimodal fluorescence analysis platforms, identifying their strengths and limitations, to establish the tools that will enable further studies on the intratumor heterogeneity and interclonal interactions in pGBM and DIPG.
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Affiliation(s)
- Giulia Pericoli
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Center, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (S.P.); (L.A.C.)
| | - Ezio Giorda
- FACs Core Facility, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy;
| | - Roberta Ferretti
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Maria Antonietta Ajmone-Cat
- National Centre for Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.A.A.-C.); (R.D.S.)
| | - Will Court
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK;
| | - Libenzio Adrian Conti
- Confocal Microscopy Core Facility, Research Center, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (S.P.); (L.A.C.)
| | - Roberta De Simone
- National Centre for Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (M.A.A.-C.); (R.D.S.)
| | - Paola Bencivenga
- Research Laboratories, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (P.B.); (A.P.)
| | - Alessia Palma
- Research Laboratories, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (P.B.); (A.P.)
| | - Angela Di Giannatale
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, Sutton SM2 5NG, UK;
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children’s Hospital—IRCCS, 00165 Rome, Italy;
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Emmanuel de Billy
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Franco Locatelli
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
| | - Maria Vinci
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital—IRCCS, 00146 Rome, Italy; (G.P.); (R.F.); (A.D.G.); (A.M.); (E.d.B.); (F.L.)
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10
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Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nat Genet 2020; 52:418-427. [PMID: 32203463 PMCID: PMC7901023 DOI: 10.1038/s41588-020-0591-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Abstract
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short alpha-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
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11
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Lee DM, Trotman JB, Cherney RE, Inoue K, Schertzer MD, Bischoff SR, Cowley DO, Calabrese JM. RETRACTED: A 5' fragment of Xist can sequester RNA produced from adjacent genes on chromatin. Nucleic Acids Res 2019; 47:7049-7062. [PMID: 31114903 PMCID: PMC6648342 DOI: 10.1093/nar/gkz432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/18/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022] Open
Abstract
Xist requires Repeat-A, a protein-binding module in its first two kilobases (2kb), to repress transcription. We report that when expressed as a standalone transcript in mouse embryonic stem cells (ESCs), the first 2kb of Xist (Xist-2kb) does not induce transcriptional silencing. Instead, Xist-2kb sequesters RNA produced from adjacent genes on chromatin. Sequestration does not spread beyond adjacent genes, requires the same sequence elements in Repeat-A that full-length Xist requires to repress transcription and can be induced by lncRNAs with similar sequence composition to Xist-2kb. We did not detect sequestration by full-length Xist, but we did detect it by mutant forms of Xist with attenuated transcriptional silencing capability. Xist-2kb associated with SPEN, a Repeat-A binding protein required for Xist-induced transcriptional silencing, but SPEN was not necessary for sequestration. Thus, when expressed in mouse ESCs, a 5' fragment of Xist that contains Repeat-A sequesters RNA from adjacent genes on chromatin and associates with the silencing factor SPEN, but it does not induce transcriptional silencing. Instead, Xist-induced transcriptional silencing requires synergy between Repeat-A and additional sequence elements in Xist. We propose that sequestration is mechanistically related to the Repeat-A dependent stabilization and tethering of Xist near actively transcribed regions of chromatin.
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Affiliation(s)
- David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jackson B Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel E Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven R Bischoff
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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12
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Stancill JS, Osipovich AB, Cartailler JP, Magnuson MA. Transgene-associated human growth hormone expression in pancreatic β-cells impairs identification of sex-based gene expression differences. Am J Physiol Endocrinol Metab 2019; 316:E196-E209. [PMID: 30532991 PMCID: PMC6397359 DOI: 10.1152/ajpendo.00229.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorescent protein reporter genes are widely used to identify and sort murine pancreatic β-cells. In this study, we compared use of the MIP-GFP transgene, which exhibits aberrant expression of human growth hormone (hGH), with a newly derived Ins2Apple allele that lacks hGH expression on the expression of sex-specific genes. β-Cells from MIP-GFP transgenic mice exhibit changes in the expression of 7,733 genes, or greater than half of their transcriptome, compared with β-cells from Ins2Apple/+ mice. To determine how these differences might affect a typical differential gene expression study, we analyzed the effect of sex on gene expression using both reporter lines. Six hundred fifty-seven differentially expressed genes were identified between male and female β-cells containing the Ins2Apple allele. Female β-cells exhibit higher expression of Xist, Tmed9, Arpc3, Eml2, and several islet-enriched transcription factors, including Nkx2-2 and Hnf4a, whereas male β-cells exhibited a generally higher expression of genes involved in cell cycle regulation. In marked contrast, the same male vs. female comparison of β-cells containing the MIP-GFP transgene revealed only 115 differentially expressed genes, and comparison of the 2 lists of differentially expressed genes revealed only 17 that were common to both analyses. These results indicate that 1) male and female β-cells differ in their expression of key transcription factors and cell cycle regulators and 2) the MIP-GFP transgene may attenuate sex-specific differences that distinguish male and female β-cells, thereby impairing the identification of sex-specific variations.
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Affiliation(s)
- Jennifer S Stancill
- Department of Cell and Developmental Biology, Vanderbilt University , Nashville, Tennessee
- Center for Stem Cell Biology, Vanderbilt University , Nashville, Tennessee
| | - Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University , Nashville, Tennessee
- Center for Stem Cell Biology, Vanderbilt University , Nashville, Tennessee
| | | | - Mark A Magnuson
- Department of Cell and Developmental Biology, Vanderbilt University , Nashville, Tennessee
- Department of Molecular Physiology and Biophysics, Vanderbilt University , Nashville, Tennessee
- Center for Stem Cell Biology, Vanderbilt University , Nashville, Tennessee
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13
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Cigliola V, Ghila L, Thorel F, van Gurp L, Baronnier D, Oropeza D, Gupta S, Miyatsuka T, Kaneto H, Magnuson MA, Osipovich AB, Sander M, Wright CEV, Thomas MK, Furuyama K, Chera S, Herrera PL. Pancreatic islet-autonomous insulin and smoothened-mediated signalling modulate identity changes of glucagon + α-cells. Nat Cell Biol 2018; 20:1267-1277. [PMID: 30361701 PMCID: PMC6215453 DOI: 10.1038/s41556-018-0216-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 09/17/2018] [Indexed: 02/06/2023]
Abstract
The mechanisms that restrict regeneration and maintain cell identity following injury are poorly characterized in higher vertebrates. Following β-cell loss, 1-2% of the glucagon-producing α-cells spontaneously engage in insulin production in mice. Here we explore the mechanisms inhibiting α-cell plasticity. We show that adaptive α-cell identity changes are constrained by intra-islet insulin- and Smoothened-mediated signalling, among others. The combination of β-cell loss or insulin-signalling inhibition, with Smoothened inactivation in α- or δ-cells, stimulates insulin production in more α-cells. These findings suggest that the removal of constitutive 'brake signals' is crucial to neutralize the refractoriness to adaptive cell-fate changes. It appears that the maintenance of cell identity is an active process mediated by repressive signals, which are released by neighbouring cells and curb an intrinsic trend of differentiated cells to change.
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Affiliation(s)
- Valentina Cigliola
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Luiza Ghila
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Clinical Science and KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Fabrizio Thorel
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Léon van Gurp
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Delphine Baronnier
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Daniel Oropeza
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simone Gupta
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Takeshi Miyatsuka
- Department of Metabolism and Endocrinology, Graduate School of Medicine , Juntendo University , Tokyo, Japan
| | - Hideaki Kaneto
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mark A Magnuson
- Departments of Molecular Physiology and Biophysics, Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Anna B Osipovich
- Departments of Molecular Physiology and Biophysics, Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Maike Sander
- Department of Pediatrics and Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Christopher E V Wright
- Department of Cell and Developmental Biology, Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Melissa K Thomas
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Kenichiro Furuyama
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simona Chera
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Clinical Science and KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Pedro L Herrera
- Department of Genetic Medicine and Development, iGE3 and Centre facultaire du diabète, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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14
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Site-specific chromosomal gene insertion: Flp recombinase versus Cas9 nuclease. Sci Rep 2017; 7:17771. [PMID: 29259215 PMCID: PMC5736728 DOI: 10.1038/s41598-017-17651-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/24/2017] [Indexed: 12/16/2022] Open
Abstract
Site-specific recombination systems like those based on the Flp recombinase proved themselves as efficient tools for cell line engineering. The recent emergence of designer nucleases, especially RNA guided endonucleases like Cas9, has considerably broadened the available toolbox for applications like targeted transgene insertions. Here we established a recombinase-mediated cassette exchange (RMCE) protocol for the fast and effective, drug-free isolation of recombinant cells. Distinct fluorescent protein patterns identified the recombination status of individual cells. In derivatives of a CHO master cell line the expression of the introduced transgene of interest could be dramatically increased almost 20-fold by subsequent deletion of the fluorescent protein gene that provided the initial isolation principle. The same master cell line was employed in a comparative analysis using CRISPR/Cas9 for transgene integration in identical loci. Even though the overall targeting efficacy was comparable, multi-loci targeting was considerably more effective for Cas9-mediated transgene insertion when compared to RMCE. While Cas9 is inherently more flexible, our results also alert to the risk of aberrant recombination events around the cut site. Together, this study points at the individual strengths in performance of both systems and provides guidance for their appropriate use.
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15
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Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming. Cell Rep 2017; 17:2028-2041. [PMID: 27851966 DOI: 10.1016/j.celrep.2016.10.068] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 09/06/2016] [Accepted: 10/19/2016] [Indexed: 12/11/2022] Open
Abstract
Using a transgenic mouse model to express MafA, Pdx1, and Neurog3 (3TF) in a pancreatic acinar cell- and doxycycline-dependent manner, we discovered that the outcome of transcription factor-mediated acinar to β-like cellular reprogramming is dependent on both the magnitude of 3TF expression and on reprogramming-induced inflammation. Overly robust 3TF expression causes acinar cell necrosis, resulting in marked inflammation and acinar-to-ductal metaplasia. Generation of new β-like cells requires limiting reprogramming-induced inflammation, either by reducing 3TF expression or by eliminating macrophages. The new β-like cells were able to reverse streptozotocin-induced diabetes 6 days after inducing 3TF expression but failed to sustain their function after removal of the reprogramming factors.
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16
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Sinha M, Lowell CA. Efficiency and Specificity of Gene Deletion in Lung Epithelial Doxycycline-Inducible Cre Mice. Am J Respir Cell Mol Biol 2017; 57:248-257. [PMID: 28287822 DOI: 10.1165/rcmb.2016-0208oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The transgenic mouse strains surfactant protein C-reverse tetracycline transactivator (SP-C-rtTA), club cell secretory protein (CCSP)-rtTA, and tetracycline operator (TetO)-Cre have been invaluable for spatiotemporally regulating gene deletion in the pulmonary epithelium. In this study, we measured the efficiency and specificity of gene deletion that can be achieved in these mice using the Rosa26-eYFP reporter. Triple-transgenic mice (tTg or rtTA/TetO-Cre/Rosa-eYFP) were bred and treated with various doxycycline (dox) regimens to induce gene deletion, which was then quantified in various cell populations by flow cytometry. In these crosses, we found that the TetO-Cre transgene must be transmitted through the female parent to avoid germline gene deletion. With dox exposure during lung development, SP-C-tTg mice deleted in ∼65-75% of alveolar epithelial type II (ATII) cells, but in only ∼45-50% of the integrin β4+ population, which consisted of club cells and distal lung progenitor cells. In contrast, CCSP-tTg mice deleted in ∼50% of ATII cells and ∼80% of integrin β4+ cells. Upon dox treatment of adults, deletion in ATII cells and integrin β4+ cells in SP-C-tTg mice dropped significantly to ∼20% and ∼6%, respectively, whereas CCSP-tTg mice deleted in ∼57% of ATII and ∼40% of integrin β4+ cells. Interestingly, untreated CCSP-tTg mice also deleted in ∼40% of integrin β4+ cells, indicating significant leakiness of CCSP-tTg in β4+ cells. In all mouse groups, minimal deletion occurred in mouse tracheal epithelial cells or in mesenchymal or hematopoietic cells. These data provide the first quantitative, side-by-side comparison of the deletion efficiency for these widely used transgenic mouse strains.
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Affiliation(s)
- Meenal Sinha
- Department of Laboratory Medicine and Program in Immunology, University of California, San Francisco, California
| | - Clifford A Lowell
- Department of Laboratory Medicine and Program in Immunology, University of California, San Francisco, California
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17
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O'Neal WK. Lung Cell-Specific Cre Deleter Mouse Strains: Going Back to Move Forward. Am J Respir Cell Mol Biol 2017; 57:149-150. [PMID: 28762768 DOI: 10.1165/rcmb.2017-0099ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Wanda K O'Neal
- 1 Marsico Lung Institute/UNC Cystic Fibrosis Center University of North Carolina at Chapel Hill Chapel Hill, North Carolina
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18
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Abstract
The hostile environment of the microscope stage poses numerous challenges to successful imaging of morphogenesis in live tissues. This review aims to highlight some of the main practical considerations to take into account when embarking on a project to image cell behaviour in the context of cells' normal surroundings. Scrutiny of these activities is likely to be the most informative approach to understanding mechanical morphogenesis but is often confounded by the substantial technical difficulties involved in imaging samples over extended periods of time. Repeated observation of cells in live tissue requires that strategies be adopted to prioritize the stability of the sample, ensuring that it remains viable and develops normally while being held in a manner accessible to microscopic examination. Key considerations when creating reliable protocols for time-lapse imaging may be broken down into three main criteria; labelling, mounting and image acquisition. Choices and compromises made here, however, will directly influence image quality, and even small refinements can substantially improve what information may be extracted from images. Live imaging of tissue is difficult but paying close attention to the basics along with a little innovation is likely to be well rewarded.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.
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Affiliation(s)
- Donald M Bell
- The Francis Crick Institute Mill Hill Laboratories, The Ridgeway, Mill Hill, London NW7 1AA, UK
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19
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Mohme M, Maire CL, Riecken K, Zapf S, Aranyossy T, Westphal M, Lamszus K, Fehse B. Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity. Mol Ther 2017; 25:621-633. [PMID: 28109958 PMCID: PMC5363186 DOI: 10.1016/j.ymthe.2016.12.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/10/2016] [Accepted: 12/12/2016] [Indexed: 11/29/2022] Open
Abstract
Intratumoral heterogeneity has been identified as one of the strongest drivers of treatment resistance and tumor recurrence. Therefore, investigating the complex clonal architecture of tumors over time has become a major challenge in cancer research. We developed a new fluorescent "optical barcoding" technique that allows fast tracking, identification, and quantification of live cell clones in vitro and in vivo using flow cytometry (FC). We optically barcoded two cell lines derived from malignant glioma, an exemplary heterogeneous brain tumor. In agreement with mathematical combinatorics, we demonstrate that up to 41 clones can unambiguously be marked using six fluorescent proteins and a maximum of three colors per clone. We show that optical barcoding facilitates sensitive, precise, rapid, and inexpensive analysis of clonal composition kinetics of heterogeneous cell populations by FC. We further assessed the quantitative contribution of multiple clones to glioblastoma growth in vivo and we highlight the potential to recover individual viable cell clones by fluorescence-activated cell sorting. In summary, we demonstrate that optical barcoding is a powerful technique for clonal cell tracking in vitro and in vivo, rendering this approach a potent tool for studying the heterogeneity of complex tissues, in particular, cancer.
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Affiliation(s)
- Malte Mohme
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cecile L Maire
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Svenja Zapf
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tim Aranyossy
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Manfred Westphal
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Katrin Lamszus
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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20
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Osipovich AB, Gangula R, Vianna PG, Magnuson MA. Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation. Development 2016; 143:4595-4607. [PMID: 27864380 PMCID: PMC5201031 DOI: 10.1242/dev.141465] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/06/2016] [Indexed: 02/02/2023]
Abstract
SET domain-containing proteins play a vital role in regulating gene expression during development through modifications in chromatin structure. Here we show that SET domain-containing 5 (Setd5) is divergently transcribed with Gt(ROSA26)Sor, is necessary for mammalian development, and interacts with the PAF1 co-transcriptional complex and other proteins. Setd5-deficient mouse embryos exhibit severe defects in neural tube formation, somitogenesis and cardiac development, have aberrant vasculogenesis in embryos, yolk sacs and placentas, and die between embryonic day 10.5 and 11.5. Setd5-deficient embryonic stem cells have impaired cellular proliferation, increased apoptosis, defective cell cycle progression, a diminished ability to differentiate into cardiomyocytes and greatly perturbed gene expression. SETD5 co-immunoprecipitates with multiple components of the PAF1 and histone deacetylase-containing NCoR complexes and is not solely required for major histone lysine methylation marks. In the absence of Setd5, histone acetylation is increased at transcription start sites and near downstream regions. These findings suggest that SETD5 functions in a manner similar to yeast Set3p and Drosophila UpSET, and that it is essential for regulating histone acetylation during gene transcription.
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Affiliation(s)
- Anna B Osipovich
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama Gangula
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Pedro G Vianna
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A Magnuson
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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21
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Abstract
The advent of fluorescent proteins (FPs) for genetic labeling of molecules and cells has revolutionized fluorescence microscopy. Genetic manipulations have created a vast array of bright and stable FPs spanning blue to red spectral regions. Common to autofluorescent FPs is their tight β-barrel structure, which provides the rigidity and chemical environment needed for effectual fluorescence. Despite the common structure, each FP has unique properties. Thus, there is no single 'best' FP for every circumstance, and each FP has advantages and disadvantages. To guide decisions about which FP is right for a given application, we have quantitatively characterized the brightness, photostability, pH stability and monomeric properties of more than 40 FPs to enable straightforward and direct comparison between them. We focus on popular and/or top-performing FPs in each spectral region.
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22
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Korobko IV, Georgiev PG, Skryabin KG, Kirpichnikov MP. GMOs in Russia: Research, Society and Legislation. Acta Naturae 2016; 8:6-13. [PMID: 28050262 PMCID: PMC5199202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Russian legislation lags behind the rapid developments witnessed in genetic engineering. Only a scientifically based and well-substantiated policy on the place of organisms that are created with the use of genetic engineering technologies and an assessment of the risks associated with them could guarantee that the breakthroughs achieved in modern genetic engineering technologies are effectively put to use in the real economy. A lack of demand for such breakthroughs in the practical field will lead to stagnation in scientific research and to a loss of expertise.
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Affiliation(s)
- I. V. Korobko
- Institute of Gene Biology RAS, Vavilova Str. 34/5, 119334, Moscow, Russia
| | - P. G. Georgiev
- Institute of Gene Biology RAS, Vavilova Str. 34/5, 119334, Moscow, Russia
| | - K. G. Skryabin
- The Federal Research Centre “Fundamentals of Biotechnology” RAS, Leninskii prospect Str. 33, build. 2, 119071, Moscow, Russia
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23
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Golson ML, Dunn JC, Maulis MF, Dadi PK, Osipovich AB, Magnuson MA, Jacobson DA, Gannon M. Activation of FoxM1 Revitalizes the Replicative Potential of Aged β-Cells in Male Mice and Enhances Insulin Secretion. Diabetes 2015; 64:3829-38. [PMID: 26251404 PMCID: PMC4613976 DOI: 10.2337/db15-0465] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/26/2015] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes incidence increases with age, while β-cell replication declines. The transcription factor FoxM1 is required for β-cell replication in various situations, and its expression declines with age. We hypothesized that increased FoxM1 activity in aged β-cells would rejuvenate proliferation. Induction of an activated form of FoxM1 was sufficient to increase β-cell mass and proliferation in 12-month-old male mice after just 2 weeks. Unexpectedly, at 2 months of age, induction of activated FoxM1 in male mice improved glucose homeostasis with unchanged β-cell mass. Cells expressing activated FoxM1 demonstrated enhanced glucose-stimulated Ca2+ influx, which resulted in improved glucose tolerance through enhanced β-cell function. Conversely, our laboratory has previously demonstrated that mice lacking FoxM1 in the pancreas display glucose intolerance or diabetes with only a 60% reduction in β-cell mass, suggesting that the loss of FoxM1 is detrimental to β-cell function. Ex vivo insulin secretion was therefore examined in size-matched islets from young mice lacking FoxM1 in β-cells. Foxm1-deficient islets indeed displayed reduced insulin secretion. Our studies reveal that activated FoxM1 increases β-cell replication while simultaneously enhancing insulin secretion and improving glucose homeostasis, making FoxM1 an attractive therapeutic target for diabetes.
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Affiliation(s)
- Maria L Golson
- VA Tennessee Valley Healthcare System, Nashville, TN Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Jennifer C Dunn
- VA Tennessee Valley Healthcare System, Nashville, TN Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Matthew F Maulis
- VA Tennessee Valley Healthcare System, Nashville, TN Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Prasanna K Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN Vanderbilt Center for Stem Cell Biology, Vanderbilt University Medical Center, Nashville, TN
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN Vanderbilt Center for Stem Cell Biology, Vanderbilt University Medical Center, Nashville, TN
| | - David A Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Maureen Gannon
- VA Tennessee Valley Healthcare System, Nashville, TN Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
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A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells. Cell Rep 2015; 13:326-36. [PMID: 26440894 DOI: 10.1016/j.celrep.2015.08.082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/10/2015] [Accepted: 08/29/2015] [Indexed: 01/05/2023] Open
Abstract
The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox9 as cooperative inducers of a gene regulatory network that distinguishes the pancreatic from the intestinal lineage. Genetic studies demonstrate dual and cooperative functions for Pdx1 and Sox9 in pancreatic lineage induction and repression of the intestinal lineage choice. Pdx1 and Sox9 bind to regulatory sequences near pancreatic and intestinal differentiation genes and jointly regulate their expression, revealing direct cooperative roles for Pdx1 and Sox9 in gene activation and repression. Our study identifies Pdx1 and Sox9 as important regulators of a transcription factor network that initiates pancreatic fate and sheds light on the gene regulatory circuitry that governs the development of distinct organs from multi-lineage-competent foregut progenitors.
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25
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Tantirigama MLS, Oswald MJ, Clare AJ, Wicky HE, Day RC, Hughes SM, Empson RM. Fezf2 expression in layer 5 projection neurons of mature mouse motor cortex. J Comp Neurol 2015; 524:829-45. [PMID: 26234885 DOI: 10.1002/cne.23875] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
The mature cerebral cortex contains a wide diversity of neuron phenotypes. This diversity is specified during development by neuron-specific expression of key transcription factors, some of which are retained for the life of the animal. One of these key developmental transcription factors that is also retained in the adult is Fezf2, but the neuron types expressing it in the mature cortex are unknown. With a validated Fezf2-Gfp reporter mouse, whole-cell electrophysiology with morphology reconstruction, cluster analysis, in vivo retrograde labeling, and immunohistochemistry, we identify a heterogeneous population of Fezf2(+) neurons in both layer 5A and layer 5B of the mature motor cortex. Functional electrophysiology identified two distinct subtypes of Fezf2(+) neurons that resembled pyramidal tract projection neurons (PT-PNs) and intratelencephalic projection neurons (IT-PNs). Retrograde labeling confirmed the former type to include corticospinal projection neurons (CSpPNs) and corticothalamic projection neurons (CThPNs), whereas the latter type included crossed corticostriatal projection neurons (cCStrPNs) and crossed-corticocortical projection neurons (cCCPNs). The two Fezf2(+) subtypes expressed either CTIP2 or SATB2 to distinguish their physiological identity and confirmed that specific expression combinations of key transcription factors persist in the mature motor cortex. Our findings indicate a wider role for Fezf2 within gene expression networks that underpin the diversity of layer 5 cortical projection neurons.
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Affiliation(s)
- Malinda L S Tantirigama
- Department of Physiology, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Manfred J Oswald
- Department of Physiology, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Alison J Clare
- Department of Biochemistry, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Hollie E Wicky
- Department of Biochemistry, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Robert C Day
- Department of Biochemistry, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Stephanie M Hughes
- Department of Biochemistry, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
| | - Ruth M Empson
- Department of Physiology, Brain Health Research Centre, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand, 9054
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26
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Osipovich AB, Long Q, Manduchi E, Gangula R, Hipkens SB, Schneider J, Okubo T, Stoeckert CJ, Takada S, Magnuson MA. Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. Development 2014; 141:2939-49. [PMID: 25053427 PMCID: PMC4197673 DOI: 10.1242/dev.104810] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Insulinoma associated 1 (Insm1) plays an important role in regulating the development of cells in the central and peripheral nervous systems, olfactory epithelium and endocrine pancreas. To better define the role of Insm1 in pancreatic endocrine cell development we generated mice with an Insm1GFPCre reporter allele and used them to study Insm1-expressing and null populations. Endocrine progenitor cells lacking Insm1 were less differentiated and exhibited broad defects in hormone production, cell proliferation and cell migration. Embryos lacking Insm1 contained greater amounts of a non-coding Neurog3 mRNA splice variant and had fewer Neurog3/Insm1 co-expressing progenitor cells, suggesting that Insm1 positively regulates Neurog3. Moreover, endocrine progenitor cells that express either high or low levels of Pdx1, and thus may be biased towards the formation of specific cell lineages, exhibited cell type-specific differences in the genes regulated by Insm1. Analysis of the function of Ripply3, an Insm1-regulated gene enriched in the Pdx1-high cell population, revealed that it negatively regulates the proliferation of early endocrine cells. Taken together, these findings indicate that in developing pancreatic endocrine cells Insm1 promotes the transition from a ductal progenitor to a committed endocrine cell by repressing a progenitor cell program and activating genes essential for RNA splicing, cell migration, controlled cellular proliferation, vasculogenesis, extracellular matrix and hormone secretion.
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Affiliation(s)
- Anna B Osipovich
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, NY 14850, USA
| | - Elisabetta Manduchi
- Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Rama Gangula
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Susan B Hipkens
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Judsen Schneider
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tadashi Okubo
- Department of Laboratory Animal Science, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan
| | - Christian J Stoeckert
- Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Shinji Takada
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Mark A Magnuson
- Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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27
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Balderes DA, Magnuson MA, Sussel L. Nkx2.2:Cre knock-in mouse line: a novel tool for pancreas- and CNS-specific gene deletion. Genesis 2013; 51:844-51. [PMID: 23996959 DOI: 10.1002/dvg.22715] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 11/07/2022]
Abstract
Nkx2.2 is a homeodomain-containing transcriptional regulator necessary for the appropriate differentiation of ventral neuronal populations in the spinal cord and hindbrain, and endocrine cell populations in the pancreas and intestine. In each tissue, Nkx2.2 inactivation leads to reciprocal cell fate alterations. To confirm the cell fate changes are due to respecification of Nkx2.2-expressing progenitors and to provide a novel tool for lineage tracing in the pancreas and CNS, we generated an Nkx2.2:Cre mouse line by knocking in a Cre-EGFP cassette into the Nkx2.2 genomic locus and inactivating endogenous Nkx2.2. The R26R-CAG-LSL-tdTomato reporter was used to monitor the specificity and efficiency of Nkx2.2:Cre activity; the tomato reporter faithfully recapitulated endogenous Nkx2.2 expression and could be detected as early as embryonic day (e) 9.25 in the developing CNS and was initiated shortly thereafter at e9.5 in the pancreas. Lineage analyses in the CNS confirmed the cell populations thought to be derived from Nkx2.2-expressing progenitor domains. Furthermore, lineage studies verified Nkx2.2 expression in the earliest pancreatic progenitors that give rise to all cell types of the pancreas; however they also revealed more robust Cre activity in the dorsal versus ventral pancreas. Thus, the Nkx2.2:Cre line provides a novel tool for gene manipulations in the CNS and pancreas.
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Affiliation(s)
- Dina A Balderes
- Department of Genetics and Development, Columbia University, New York, New York, 10032
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28
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Kartikasari AER, Zhou JX, Kanji MS, Chan DN, Sinha A, Grapin-Botton A, Magnuson MA, Lowry WE, Bhushan A. The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation. EMBO J 2013; 32:1393-408. [PMID: 23584530 DOI: 10.1038/emboj.2013.78] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 03/13/2013] [Indexed: 02/07/2023] Open
Abstract
Stem cell differentiation depends on transcriptional activation driven by lineage-specific regulators as well as changes in chromatin organization. However, the coordination of these events is poorly understood. Here, we show that T-box proteins team up with chromatin modifying enzymes to drive the expression of the key lineage regulator, Eomes during endodermal differentiation of embryonic stem (ES) cells. The Eomes locus is maintained in a transcriptionally poised configuration in ES cells. During early differentiation steps, the ES cell factor Tbx3 associates with the histone demethylase Jmjd3 at the enhancer element of the Eomes locus to allow enhancer-promoter interactions. This spatial reorganization of the chromatin primes the cells to respond to Activin signalling, which promotes the binding of Jmjd3 and Eomes to its own bivalent promoter region to further stimulate Eomes expression in a positive feedback loop. In addition, Eomes activates a transcriptional network of core regulators of endodermal differentiation. Our results demonstrate that Jmjd3 sequentially associates with two T-box factors, Tbx3 and Eomes to drive stem cell differentiation towards the definitive endoderm lineage.
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29
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Hanson CA, Drake KR, Baird MA, Han B, Kraft LJ, Davidson MW, Kenworthy AK. Overexpression of caveolin-1 is sufficient to phenocopy the behavior of a disease-associated mutant. Traffic 2013; 14:663-77. [PMID: 23469926 DOI: 10.1111/tra.12066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 03/05/2013] [Accepted: 03/07/2013] [Indexed: 12/30/2022]
Abstract
Mutations and alterations in caveolin-1 expression levels have been linked to a number of human diseases. How misregulation of caveolin-1 contributes to disease is not fully understood, but has been proposed to involve the intracellular accumulation of mutant forms of the protein. To better understand the molecular basis for trafficking defects that trap caveolin-1 intracellularly, we compared the properties of a GFP-tagged version of caveolin-1 P132L, a mutant form of caveolin-1 previously linked to breast cancer, with wild-type caveolin-1. Unexpectedly, wild-type caveolin-1-GFP also accumulated intracellularly, leading us to examine the mechanisms underlying the abnormal localization of the wild type and mutant protein in more detail. We show that both the nature of the tag and cellular context impact the subcellular distribution of caveolin-1, demonstrate that even the wild-type form of caveolin-1 can function as a dominant negative under some conditions, and identify specific conformation changes associated with incorrectly targeted forms of the protein. In addition, we find intracellular caveolin-1 is phosphorylated on Tyr14, but phosphorylation is not required for mistrafficking of the protein. These findings identify novel properties of mistargeted forms of caveolin-1 and raise the possibility that common trafficking defects underlie diseases associated with overexpression and mutations in caveolin-1.
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Affiliation(s)
- Caroline A Hanson
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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30
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Choi E, Kraus MRC, Lemaire LA, Yoshimoto M, Vemula S, Potter LA, Manduchi E, Stoeckert CJ, Grapin-Botton A, Magnuson MA. Dual lineage-specific expression of Sox17 during mouse embryogenesis. Stem Cells 2013; 30:2297-308. [PMID: 22865702 DOI: 10.1002/stem.1192] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Sox17 is essential for both endoderm development and fetal hematopoietic stem cell (HSC) maintenance. While endoderm-derived organs are well known to originate from Sox17-expressing cells, it is less certain whether fetal HSCs also originate from Sox17-expressing cells. By generating a Sox17(GFPCre) allele and using it to assess the fate of Sox17-expressing cells during embryogenesis, we confirmed that both endodermal and a part of definitive hematopoietic cells are derived from Sox17-positive cells. Prior to E9.5, the expression of Sox17 is restricted to the endoderm lineage. However, at E9.5 Sox17 is expressed in the endothelial cells (ECs) at the para-aortic splanchnopleural region that contribute to the formation of HSCs at a later stage. The identification of two distinct progenitor cell populations that express Sox17 at E9.5 was confirmed using fluorescence-activated cell sorting together with RNA-Seq to determine the gene expression profiles of the two cell populations. Interestingly, this analysis revealed differences in the RNA processing of the Sox17 mRNA during embryogenesis. Taken together, these results indicate that Sox17 is expressed in progenitor cells derived from two different germ layers, further demonstrating the complex expression pattern of this gene and suggesting caution when using Sox17 as a lineage-specific marker.
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Affiliation(s)
- Eunyoung Choi
- Center for Stem Cell Biology and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232-0494, USA
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31
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Ghrelin expression in the mouse pancreas defines a unique multipotent progenitor population. PLoS One 2012; 7:e52026. [PMID: 23251675 PMCID: PMC3520898 DOI: 10.1371/journal.pone.0052026] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 11/13/2012] [Indexed: 01/01/2023] Open
Abstract
Pancreatic islet cells provide the major source of counteractive endocrine hormones required for maintaining glucose homeostasis; severe health problems result when these cell types are insufficiently active or reduced in number. Therefore, the process of islet endocrine cell lineage allocation is critical to ensure there is a correct balance of islet cell types. There are four endocrine cell types within the adult islet, including the glucagon-producing alpha cells, insulin-producing beta cells, somatostatin-producing delta cells and pancreatic polypeptide-producing PP cells. A fifth islet cell type, the ghrelin-producing epsilon cells, is primarily found during gestational development. Although hormone expression is generally assumed to mark the final entry to a determined cell state, we demonstrate in this study that ghrelin-expressing epsilon cells within the mouse pancreas do not represent a terminally differentiated endocrine population. Ghrelin cells give rise to significant numbers of alpha and PP cells and rare beta cells in the adult islet. Furthermore, pancreatic ghrelin-producing cells are maintained in pancreata lacking the essential endocrine lineage regulator Neurogenin3, and retain the ability to contribute to cells within the pancreatic ductal and exocrine lineages. These results demonstrate that the islet ghrelin-expressing epsilon cells represent a multi-potent progenitor cell population that delineates a major subgrouping of the islet endocrine cell populations. These studies also provide evidence that many of hormone-producing cells within the adult islet represent heterogeneous populations based on their ontogeny, which could have broader implications on the regulation of islet cell ratios and their ability to effectively respond to fluctuations in the metabolic environment during development.
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32
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Serup P, Gustavsen C, Klein T, Potter LA, Lin R, Mullapudi N, Wandzioch E, Hines A, Davis A, Bruun C, Engberg N, Petersen DR, Peterslund JML, Macdonald RJ, Grapin-Botton A, Magnuson MA, Zaret KS. Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice. Dis Model Mech 2012; 5:956-66. [PMID: 22888097 PMCID: PMC3484877 DOI: 10.1242/dmm.009696] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Extracellular signals in development, physiology, homeostasis and disease often act by regulating transcription. Herein we describe a general method and specific resources for determining where and when such signaling occurs in live animals and for systematically comparing the timing and extent of different signals in different cellular contexts. We used recombinase-mediated cassette exchange (RMCE) to test the effect of successively deleting conserved genomic regions of the ubiquitously active Rosa26 promoter and substituting the deleted regions for regulatory sequences that respond to diverse extracellular signals. We thereby created an allelic series of embryonic stem cells and mice, each containing a signal-responsive sentinel with different fluorescent reporters that respond with sensitivity and specificity to retinoic acids, bone morphogenic proteins, activin A, Wnts or Notch, and that can be adapted to any pathway that acts via DNA elements.
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Affiliation(s)
- Palle Serup
- Hagedorn Research Institute, Department of Developmental Biology, Niels Steensens Vej 6, DK-2820, Denmark
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33
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Arnes L, Leclerc K, Friel JM, Hipkens SB, Magnuson MA, Sussel L. Generation of Nkx2.2:lacZ mice using recombination-mediated cassette exchange technology. Genesis 2012; 50:612-24. [PMID: 22539496 DOI: 10.1002/dvg.22037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 04/16/2012] [Accepted: 04/19/2012] [Indexed: 11/08/2022]
Abstract
Nkx2.2 encodes a homeodomain transcription factor required for the correct specification and/or differentiation of cells in the pancreas, intestine, and central nervous system (CNS). To follow the fate of cells deleted for Nkx2.2 within these tissues, we generated Nkx2.2:lacZ knockin mice using a recombination-mediated cassette exchange (RMCE) approach. Expression analysis of lacZ and/or β-galactosidase in Nkx2.2(lacZ/+) heterozygote embryos and adults demonstrates that lacZ faithfully recapitulates endogenous Nkx2.2 expression. Furthermore, the Nkx2.2(lacZ/lacZ) homozygous embryos display phenotypes indistinguishable from the previously characterized Nkx2.2(-/-) strain. LacZ expression analyses in the Nkx2.2(lacZ/lacZ) homozygous embryos indicate that Nkx2.2-expressing progenitor cells within the pancreas are generated in their normal numbers and are not mislocalized within the pancreatic ductal epithelium or developing islets. In the CNS of Nkx2.2(lacZ/lacZ) embryos, LacZ-expressing cells within the ventral P3 progenitor domain display different migration properties depending on the developmental stage and their respective differentiation potential.
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Affiliation(s)
- Luis Arnes
- Department of Genetics and Development, Columbia University, New York, New York, USA
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34
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Potter LA, Choi E, Hipkens SB, Wright CVE, Magnuson MA. A recombinase-mediated cassette exchange-derived cyan fluorescent protein reporter allele for Pdx1. Genesis 2012; 50:384-92. [PMID: 21913313 DOI: 10.1002/dvg.20804] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/02/2011] [Accepted: 09/07/2011] [Indexed: 01/13/2023]
Abstract
Fluorescent protein (FP) reporter alleles are useful both for identifying and purifying specific cell populations in the mouse. Here, we report the generation of mouse embryonic stem cells that contain a pancreatic and duodenal homeobox 1 (Pdx1) loxed cassette acceptor (Pdx1(LCA)) allele and the use of recombinase-mediated cassette exchange to derive mice that contain a Pdx1(CFP) (Cerulean) reporter allele. Mice with this allele exhibited cyan fluorescence within the previously well-characterized Pdx1 expression domain in posterior foregut endoderm. Immunolabeling showed that endogenous Pdx1 was coexpressed with CFP at all time points examined. Furthermore, fluorescence-activated cell sorting was used to isolate CFP-positive cells from E11.5 and E18.5 embryonic tissues using both 405 and 445 nm lasers, although the latter resulted in a nearly 50-fold increase in emission intensity. The Pdx1(CFP) allele will enable the isolation of specific foregut endoderm and pancreatic cell populations, both alone and in combination with other FP reporter alleles.
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Affiliation(s)
- Leah A Potter
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0494, USA
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35
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Rawlins EL, Perl AK. The a"MAZE"ing world of lung-specific transgenic mice. Am J Respir Cell Mol Biol 2011; 46:269-82. [PMID: 22180870 DOI: 10.1165/rcmb.2011-0372ps] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The purpose of this review is to give a comprehensive overview of transgenic mouse lines suitable for studying gene function and cellular lineage relationships in lung development, homeostasis, injury, and repair. Many of the mouse strains reviewed in this Perspective have been widely shared within the lung research community, and new strains are continuously being developed. There are many transgenic lines that target subsets of lung cells, but it remains a challenge for investigators to select the correct transgenic modules for their experiment. This review covers the tetracycline- and tamoxifen-inducible systems and focuses on conditional lines that target the epithelial cells. We point out the limitations of each strain so investigators can choose the system that will work best for their scientific question. Current mesenchymal and endothelial lines are limited by the fact that they are not lung specific. These lines are summarized in a brief overview. In addition, useful transgenic reporter mice for studying lineage relationships, promoter activity, and signaling pathways will complete our lung-specific conditional transgenic mouse shopping list.
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Affiliation(s)
- Emma L Rawlins
- Children's Hospital Medical Center, Divisions of Neonatology and Pulmonary Biology, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
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36
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Papizan JB, Singer RA, Tschen SI, Dhawan S, Friel JM, Hipkens SB, Magnuson MA, Bhushan A, Sussel L. Nkx2.2 repressor complex regulates islet β-cell specification and prevents β-to-α-cell reprogramming. Genes Dev 2011; 25:2291-305. [PMID: 22056672 DOI: 10.1101/gad.173039.111] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Regulation of cell differentiation programs requires complex interactions between transcriptional and epigenetic networks. Elucidating the principal molecular events responsible for the establishment and maintenance of cell fate identities will provide important insights into how cell lineages are specified and maintained and will improve our ability to recapitulate cell differentiation events in vitro. In this study, we demonstrate that Nkx2.2 is part of a large repression complex in pancreatic β cells that includes DNMT3a, Grg3, and HDAC1. Mutation of the endogenous Nkx2.2 tinman (TN) domain in mice abolishes the interaction between Nkx2.2 and Grg3 and disrupts β-cell specification. Furthermore, we demonstrate that Nkx2.2 preferentially recruits Grg3 and HDAC1 to the methylated Aristaless homeobox gene (Arx) promoter in β cells. The Nkx2.2 TN mutation results in ectopic expression of Arx in β cells, causing β-to-α-cell transdifferentiation. A corresponding β-cell-specific deletion of DNMT3a is also sufficient to cause Arx-dependent β-to-α-cell reprogramming. Notably, subsequent removal of Arx in the β cells of Nkx2.2(TNmut/TNmut) mutant mice reverts the β-to-α-cell conversion, indicating that the repressor activities of Nkx2.2 on the methylated Arx promoter in β cells are the primary regulatory events required for maintaining β-cell identity.
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Affiliation(s)
- James B Papizan
- Department of Genetics and Development, Institute of Human Nutrition, Columbia University, New York 10032, USA
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37
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Petersen DR, Gustavsen C, Lindskog SR, Magnuson MA, Zaret KS, Serup P. Engineering artificial signaling centers to polarize embryoid body differentiation. Stem Cells Dev 2011; 21:647-53. [PMID: 21958075 DOI: 10.1089/scd.2011.0344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Embryonic stem (ES) cells differentiating as aggregates self-organize dependent on Wnt signaling that is initially localized to discrete sites in the aggregate. As differentiation proceeds, Wnt signaling expands to most of the aggregates, thus resulting in widespread differentiation of mesendodermal progenitors. This process resembles primitive streak formation, but the lack of organized positional information makes the differentiating aggregates develop in a disorganized fashion. Here, we report that exogenous, cellular signaling sources can control the site where differentiation initiates in ES cell aggregates. Fibroblasts engineered to express cadherins are assembled with ES cells to form composite aggregates where the fibroblasts are positioned as a discrete pole. When engineered to express secreted Wnt agonists or antagonists, this pole functions to localize signaling in a way that polarizes the differentiating aggregates. The use of cell adhesion molecules to control morphology of developing stem cell aggregates should be widely applicable in tissue engineering.
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Affiliation(s)
- Dorthe R Petersen
- Department of Stem Cell Biology, Hagedorn Research Institute, Gentofte, Denmark
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38
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Abstract
Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function.
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Affiliation(s)
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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