1
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González-Solares EA, Dariush A, González-Fernández C, Küpcü Yoldaş A, Molaeinezhad A, Al Sa’d M, Smith L, Whitmarsh T, Millar N, Chornay N, Falciatori I, Fatemi A, Goodwin D, Kuett L, Mulvey CM, Páez Ribes M, Qosaj F, Roth A, Vázquez-García I, Watson SS, Windhager J, Aparicio S, Bodenmiller B, Boyden E, Caldas C, Harris O, Shah SP, Tavaré S, Bressan D, Hannon GJ, Walton NA. Imaging and Molecular Annotation of Xenographs and Tumours (IMAXT): High throughput data and analysis infrastructure. Biol Imaging 2023; 3:e11. [PMID: 38487685 PMCID: PMC10936408 DOI: 10.1017/s2633903x23000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/21/2022] [Accepted: 03/08/2023] [Indexed: 03/17/2024]
Abstract
With the aim of producing a 3D representation of tumors, imaging and molecular annotation of xenografts and tumors (IMAXT) uses a large variety of modalities in order to acquire tumor samples and produce a map of every cell in the tumor and its host environment. With the large volume and variety of data produced in the project, we developed automatic data workflows and analysis pipelines. We introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located, instead of bringing data to their local computers. Here, we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumor models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT. The automatic pipelines are highly optimized and allow to obtain processed datasets several times quicker than current solutions narrowing the gap between data acquisition and scientific exploitation.
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Affiliation(s)
| | - Ali Dariush
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | - Mohammad Al Sa’d
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
| | - Leigh Smith
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
| | - Tristan Whitmarsh
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
| | - Neil Millar
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Chornay
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
| | - Ilaria Falciatori
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Atefeh Fatemi
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Goodwin
- McGovern Institute, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura Kuett
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Claire M. Mulvey
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Marta Páez Ribes
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Fatime Qosaj
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Andrew Roth
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
| | - Ignacio Vázquez-García
- Herbert and Florence Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Spencer S. Watson
- Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Jonas Windhager
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ed Boyden
- McGovern Institute, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Physics, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Carlos Caldas
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | | | - Sohrab P. Shah
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon Tavaré
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
- Herbert and Florence Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Dario Bressan
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Gregory J. Hannon
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas A. Walton
- Institute of Astronomy, University of Cambridge, Cambridge, United Kingdom
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2
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Yogev O, Weissbrod O, Battistoni G, Bressan D, Naamati A, Falciatori I, Berkyurek AC, Rasnic R, Izuagbe R, Hosmillo M, Ilan S, Grossman I, McCormick L, Honeycutt CC, Johnston T, Gagne M, Douek DC, Goodfellow I, Hannon GJ, Erlich Y. From a genome-wide screen of RNAi molecules against SARS-CoV-2 to a validated broad-spectrum and potent prophylaxis. Commun Biol 2023; 6:277. [PMID: 36928598 PMCID: PMC10019795 DOI: 10.1038/s42003-023-04589-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
Expanding the arsenal of prophylactic approaches against SARS-CoV-2 is of utmost importance, specifically those strategies that are resistant to antigenic drift in Spike. Here, we conducted a screen of over 16,000 RNAi triggers against the SARS-CoV-2 genome, using a massively parallel assay to identify hyper-potent siRNAs. We selected Ten candidates for in vitro validation and found five siRNAs that exhibited hyper-potent activity (IC50 < 20 pM) and strong blockade of infectivity in live-virus experiments. We further enhanced this activity by combinatorial pairing of the siRNA candidates and identified cocktails that were active against multiple types of variants of concern (VOC). We then examined over 2,000 possible mutations in the siRNA target sites by using saturation mutagenesis and confirmed broad protection of the leading cocktail against future variants. Finally, we demonstrated that intranasal administration of this siRNA cocktail effectively attenuates clinical signs and viral measures of disease in the gold-standard Syrian hamster model. Our results pave the way for the development of an additional layer of antiviral prophylaxis that is orthogonal to vaccines and monoclonal antibodies.
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Affiliation(s)
- Ohad Yogev
- Eleven Therapeutics, Cambridge, United Kingdom.
| | | | - Giorgia Battistoni
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Dario Bressan
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Adi Naamati
- Eleven Therapeutics, Cambridge, United Kingdom
| | | | | | | | - Rhys Izuagbe
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | | | | | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Cole Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | - Gregory James Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
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3
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Yogev O, Weissbrod O, Battistoni G, Bressan D, Naamti A, Falciatori I, Berkyurek AC, Rasnic R, Hosmillo M, Ilan S, Grossman I, McCormick L, Honeycutt CC, Johnston T, Gagne M, Douek DC, Goodfellow I, Hannon GJ, Erlich Y. Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis. bioRxiv 2022:2022.04.12.488010. [PMID: 35441162 PMCID: PMC9016640 DOI: 10.1101/2022.04.12.488010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Expanding the arsenal of prophylactic approaches against SARS-CoV-2 is of utmost importance, specifically those strategies that are resistant to antigenic drift in Spike. Here, we conducted a screen with over 16,000 RNAi triggers against the SARS-CoV-2 genome using a massively parallel assay to identify hyper-potent siRNAs. We selected 10 candidates for in vitro validation and found five siRNAs that exhibited hyper-potent activity with IC50<20pM and strong neutralisation in live virus experiments. We further enhanced the activity by combinatorial pairing of the siRNA candidates to develop siRNA cocktails and found that these cocktails are active against multiple types of variants of concern (VOC). We examined over 2,000 possible mutations to the siRNA target sites using saturation mutagenesis and identified broad protection against future variants. Finally, we demonstrated that intranasal administration of the siRNA cocktail effectively attenuates clinical signs and viral measures of disease in the Syrian hamster model. Our results pave the way to development of an additional layer of antiviral prophylaxis that is orthogonal to vaccines and monoclonal antibodies.
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Affiliation(s)
- Ohad Yogev
- Eleven Therapeutics, Cambridge, United Kingdom
| | | | - Giorgia Battistoni
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
| | - Dario Bressan
- Eleven Therapeutics, Cambridge, United Kingdom
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
| | - Adi Naamti
- Eleven Therapeutics, Cambridge, United Kingdom
| | | | | | | | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | | | | | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher C. Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
| | - Gregory J. Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
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4
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Fabry MH, Ciabrelli F, Munafò M, Eastwood EL, Kneuss E, Falciatori I, Falconio FA, Hannon GJ, Czech B. piRNA-guided co-transcriptional silencing coopts nuclear export factors. eLife 2019; 8:e47999. [PMID: 31219034 PMCID: PMC6677536 DOI: 10.7554/elife.47999] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal gonads. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx); however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 or Nxt1 to RNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing.
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Affiliation(s)
- Martin H Fabry
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Filippo Ciabrelli
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Ilaria Falciatori
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Federica A Falconio
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
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5
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Rodriguez JD, Myrick DA, Falciatori I, Christopher MA, Lee TW, Hannon GJ, Katz DJ. A Model for Epigenetic Inhibition via Transvection in the Mouse. Genetics 2017; 207:129-138. [PMID: 28696215 PMCID: PMC5586367 DOI: 10.1534/genetics.117.201913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/21/2017] [Indexed: 01/21/2023] Open
Abstract
Transvection is broadly defined as the ability of one locus to affect its homologous locus in trans Although it was first discovered in the 1950s, there are only two known cases in mammals. Here, we report another instance of mammalian transvection induced by the Cre/LoxP system, which is widely used for conditional gene targeting in the mouse. We attempted to use the germline-expressed Vasa-Cre transgene to engineer a mouse mutation, but observe a dramatic reduction of LoxP recombination in mice that inherit an already deleted LoxP allele in trans A similar phenomenon has previously been observed with another Cre that is expressed during meiosis: Sycp-1-Cre This second example of LoxP inhibition in trans reinforces the conclusion that certain meiotically expressed Cre alleles can initiate transvection in mammals. However, unlike the previous example, we find that the inhibition of LoxP recombination is not due to DNA methylation. In addition, we demonstrate that LoxP inhibition is easily alleviated by adding an extra generation to our crossing scheme. This finding confirms that the LoxP sites are inhibited via an epigenetic mechanism, and provides a method for the use of other Cre transgenes associated with a similar LoxP inhibition event. Furthermore, the abrogation of LoxP inhibition by the simple addition of an extra generation in our crosses establishes a unique mouse system for future studies to uncover the mechanism of transvection in mammals.
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Affiliation(s)
- Juan D Rodriguez
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Dexter A Myrick
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Ilaria Falciatori
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom
| | | | - Teresa W Lee
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom
| | - David J Katz
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
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6
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Fagegaltier D, Falciatori I, Czech B, Castel S, Perrimon N, Simcox A, Hannon GJ. Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway. Genes Dev 2016; 30:1623-35. [PMID: 27474441 PMCID: PMC4973292 DOI: 10.1101/gad.284927.116] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022]
Abstract
Germline genes often become re-expressed in soma-derived human cancers as "cancer/testis antigens" (CTAs), and piRNA (PIWI-interacting RNA) pathway proteins are found among CTAs. However, whether and how the piRNA pathway contributes to oncogenesis in human neoplasms remain poorly understood. We found that oncogenic Ras combined with loss of the Hippo tumor suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from annotated generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also altered expression of some protein-coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that, at least in this context, the piRNA pathway may play a functional role in cancer.
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Affiliation(s)
- Delphine Fagegaltier
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | | | - Norbert Perrimon
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amanda Simcox
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom; The New York Genome Center, New York, New York 10011, USA
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7
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Nardacci R, Falciatori I, Moreno S, Stefanini S. Immunohistochemical Localization of Peroxisomal Enzymes During Rat Embryonic Development. J Histochem Cytochem 2016; 52:423-36. [PMID: 15033994 DOI: 10.1177/002215540405200401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Peroxisomes are cytoplasmic organelles involved in a variety of metabolic pathways. Thus far, the morphological and biochemical features of peroxisomes have been extensively characterized in adult tissues. However, the existence of congenital peroxisomal disorders, primarily affecting tissue differentiation, emphasizes the importance of these organelles in the early stages of organogenesis. We investigated the occurrence and tissue distribution of three peroxisomal enzymes in rat embryos at various developmental stages. By means of a highly sensitive biotinyl-tyramide protocol, catalase, acyl-CoA oxidase, and ketoacyl-CoA thiolase were detected in embryonic tissues where peroxisomes had not thus far been recognized, i.e., adrenal and pancreatic parenchyma, choroid plexus, neuroblasts of cranial and spinal ganglia and myenteric plexus, and chondroblasts of certain skeletal structures. In other tissues, i.e., gut epithelium and neuroblasts of some CNS areas, they were identified earlier than previously. In select CNS areas, ultrastructural catalase cytochemistry allowed identification of actively proliferating organelles at early developmental stages in several cell types. Our data show that in most organs maturation of peroxisomes parallels the acquirement of specific functions, mainly related to lipid metabolism, thus supporting an involvement of the organelles in tissue differentiation.
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Affiliation(s)
- Roberta Nardacci
- Department of Cellular and Developmental Biology, University La Sapienza, Italy.
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8
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Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M. Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. Nat Commun 2016; 7:11275. [PMID: 27117588 PMCID: PMC4853422 DOI: 10.1038/ncomms11275] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/09/2016] [Indexed: 11/29/2022] Open
Abstract
Spermatogonial stem and progenitor cells (SSCs) generate adult male gametes. During in vitro expansion, these unipotent murine cells spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs). Here we investigate this conversion process through integrative transcriptomic and epigenomic analyses. We find in SSCs that promoters essential to maintenance and differentiation of embryonic stem cells (ESCs) are enriched with histone H3-lysine4 and -lysine 27 trimethylations. These bivalent modifications are maintained at most somatic promoters after conversion, bestowing MASCs an ESC-like promoter chromatin. At enhancers, the core pluripotency circuitry is activated partially in SSCs and completely in MASCs, concomitant with loss of germ cell-specific gene expression and initiation of embryonic-like programs. Furthermore, SSCs in vitro maintain the epigenomic characteristics of germ cells in vivo. Our observations suggest that SSCs encode innate plasticity through the epigenome and that both conversion of promoter chromatin states and activation of cell type-specific enhancers are prominent features of reprogramming. Spermatogonial stem cells (SSCs) spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs). Here, the authors reveal the dynamics of bivalent histone H3-lysine4 and -lysine27 methylation signatures at somatic gene promoters in SSCs and ESC-like promoter chromatin states in MASCs.
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Affiliation(s)
- Ying Liu
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA.,Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, USA
| | - Eugenia G Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, New York 11201, USA.,Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York 10021, USA
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ilaria Falciatori
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
| | - C David Allis
- Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, USA
| | - Shahin Rafii
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Marco Seandel
- Department of Surgery, Weill Cornell Medical College, New York, New York 10065, USA
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9
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Zhou X, Battistoni G, El Demerdash O, Gurtowski J, Wunderer J, Falciatori I, Ladurner P, Schatz MC, Hannon GJ, Wasik KA. Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA 2015; 21:1885-97. [PMID: 26323280 PMCID: PMC4604429 DOI: 10.1261/rna.052456.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
PIWI proteins and piRNA pathways are essential for transposon silencing and some aspects of gene regulation during animal germline development. In contrast to most animal species, some flatworms also express PIWIs and piRNAs in somatic stem cells, where they are required for tissue renewal and regeneration. Here, we have identified and characterized piRNAs and PIWI proteins in the emerging model flatworm Macrostomum lignano. We found that M. lignano encodes at least three PIWI proteins. One of these, Macpiwi1, acts as a key component of the canonical piRNA pathway in the germline and in somatic stem cells. Knockdown of Macpiwi1 dramatically reduces piRNA levels, derepresses transposons, and severely impacts stem cell maintenance. Knockdown of the piRNA biogenesis factor Macvasa caused an even greater reduction in piRNA levels with a corresponding increase in transposons. Yet, in Macvasa knockdown animals, we detected no major impact on stem cell self-renewal. These results may suggest stem cell maintenance functions of PIWI proteins in flatworms that are distinguishable from their impact on transposons and that might function independently of what are considered canonical piRNA populations.
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Affiliation(s)
- Xin Zhou
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Giorgia Battistoni
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Julia Wunderer
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Ilaria Falciatori
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Peter Ladurner
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Michael C Schatz
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Kaja A Wasik
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
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10
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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11
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Wasik KA, Tam OH, Knott SR, Falciatori I, Hammell M, Vagin VV, Hannon GJ. RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev 2015; 29:1403-15. [PMID: 26115953 PMCID: PMC4511215 DOI: 10.1101/gad.265215.115] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/03/2015] [Indexed: 01/21/2023]
Abstract
PIWI proteins and their associated piRNAs protect germ cells from the activity of mobile genetic elements. Two classes of piRNAs—primary and secondary—are defined by their mechanisms of biogenesis. Primary piRNAs are processed directly from transcripts of piRNA cluster loci, whereas secondary piRNAs are generated in an adaptive amplification loop, termed the ping-pong cycle. In mammals, piRNA populations are dynamic, shifting as male germ cells develop. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, the piRNA population is transposon-poor and largely restricted to primary piRNAs derived from pachytene piRNA clusters. The transition from the embryonic to the adult piRNA pathway is not well understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong occurs inappropriately in meiotic cells. Ping-pong initiates piRNA responses against not only transposons but also protein-coding genes and long noncoding RNAs, including genes essential for germ cell development. Thus, the sterility of Rnf17 mutants may be a manifestation of a small RNA-based autoimmune reaction.
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Affiliation(s)
- Kaja A Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Oliver H Tam
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Simon R Knott
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Molly Hammell
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Vasily V Vagin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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12
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Goh WSS, Falciatori I, Tam OH, Burgess R, Meikar O, Kotaja N, Hammell M, Hannon GJ. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev 2015; 29:1032-44. [PMID: 25995188 PMCID: PMC4441051 DOI: 10.1101/gad.260455.115] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022]
Abstract
MIWI catalytic activity is required for spermatogenesis, indicating that piRNA-guided cleavage is critical for germ cell development. To identify meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing a human meiotic piRNA cluster. This triggered a spermatogenesis defect by inappropriately targeting the piRNA machinery to mouse mRNAs essential for germ cell development. Analysis of such de novo targets revealed a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein-coding genes as targets of native piRNAs. Cleavage of genic targets began at the pachytene stage and resulted in progressive repression through meiosis, driven at least in part via the ping-pong cycle. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells.
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Affiliation(s)
- Wee Siong Sho Goh
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oliver H Tam
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Ralph Burgess
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Oliver Meikar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Noora Kotaja
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Molly Hammell
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK;
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13
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Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. Two waves of de novo methylation during mouse germ cell development. Genes Dev 2014; 28:1544-9. [PMID: 25030694 PMCID: PMC4102761 DOI: 10.1101/gad.244350.114] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/16/2014] [Indexed: 11/24/2022]
Abstract
During development, mammalian germ cells reprogram their epigenomes via a genome-wide erasure and de novo rewriting of DNA methylation marks. We know little of how methylation patterns are specifically determined. The piRNA pathway is thought to target the bulk of retrotransposon methylation. Here we show that most retrotransposon sequences are modified by default de novo methylation. However, potentially active retrotransposon copies evade this initial wave, likely mimicking features of protein-coding genes. These elements remain transcriptionally active and become targets of piRNA-mediated methylation. Thus, we posit that these two waves play essential roles in resetting germ cell epigenomes at each generation.
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Affiliation(s)
- Antoine Molaro
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Emily Hodges
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Alexei A. Aravin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Krista Marran
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Shahin Rafii
- Ansary Stem Cell Institute, Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - W. Richard McCombie
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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14
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Ding BS, James D, Iyer R, Falciatori I, Hambardzumyan D, Wang S, Butler JM, Rabbany SY, Hormigo A. Prominin 1/CD133 endothelium sustains growth of proneural glioma. PLoS One 2013; 8:e62150. [PMID: 23637986 PMCID: PMC3636202 DOI: 10.1371/journal.pone.0062150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/18/2013] [Indexed: 11/28/2022] Open
Abstract
In glioblastoma high expression of the CD133 gene, also called Prominin1, is associated with poor prognosis. The PDGF-driven proneural group represents a subset of glioblastoma in which CD133 is not overexpressed. Interestingly, this particular subset shows a relatively good prognosis. As with many other tumors, gliobastoma is believed to arise and be maintained by a restricted population of stem-like cancer cells that express the CD133 transmembrane protein. The significance of CD133+ cells for gliomagenesis is controversial because of conflicting supporting evidence. Contributing to this inconsistency is the fact that the isolation of CD133+ cells has largely relied on the use of antibodies against ill-defined glycosylated epitopes of CD133. To overcome this problem, we used a knock-in lacZ reporter mouse, Prom1lacZ/+, to track Prom1+ cells in the brain. We found that Prom1 (prominin1, murine CD133 homologue) is expressed by cells that express markers characteristic of the neuronal, glial or vascular lineages. In proneural tumors derived from injection of RCAS-PDGF into the brains of tv-a;Ink4a-Arf−/− Prom1lacZ/+ mice, Prom1+ cells expressed markers for astrocytes or endothelial cells. Mice co-transplanted with proneural tumor sphere cells and Prom1+ endothelium had a significantly increased tumor burden and more vascular proliferation (angiogenesis) than those co-transplanted with Prom1− endothelium. We also identified specific genes in Prom1+ endothelium that code for endothelial signaling modulators that were not overexpressed in Prom1− endothelium. These factors may support proneural tumor progression and could be potential targets for anti-angiogenic therapy.
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Affiliation(s)
- Bi-Sen Ding
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Daylon James
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Rajiv Iyer
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ilaria Falciatori
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Dolores Hambardzumyan
- Department of Neurosurgery and Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Su Wang
- Department of Neurology, Center for Translational Neuromedicine, Oncology and Neurosurgery, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jason M. Butler
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Sina Y. Rabbany
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Bioengineering Program, Hofstra University, Hempstead, New York, United States of America
| | - Adília Hormigo
- Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Department of Neurology, Center for Translational Neuromedicine, Oncology and Neurosurgery, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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15
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Hobbs RM, Seandel M, Falciatori I, Rafii S, Pandolfi PP. Plzf regulates germline progenitor self-renewal by opposing mTORC1. Cell 2010; 142:468-79. [PMID: 20691905 DOI: 10.1016/j.cell.2010.06.041] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 04/01/2010] [Accepted: 05/28/2010] [Indexed: 12/25/2022]
Abstract
Hyperactivity of mTORC1, a key mediator of cell growth, leads to stem cell depletion, although the underlying mechanisms are poorly defined. Using spermatogonial progenitor cells (SPCs) as a model system, we show that mTORC1 impairs stem cell maintenance by a negative feedback from mTORC1 to receptors required to transduce niche-derived signals. We find that SPCs lacking Plzf, a transcription factor essential for SPC maintenance, have enhanced mTORC1 activity. Aberrant mTORC1 activation in Plzf(-/-) SPCs inhibits their response to GDNF, a growth factor critical for SPC self-renewal, via negative feedback at the level of the GDNF receptor. Plzf opposes mTORC1 activity by inducing expression of the mTORC1 inhibitor Redd1. Thus, we identify the mTORC1-Plzf functional interaction as a critical rheostat for maintenance of the spermatogonial pool and propose a model whereby negative feedback from mTORC1 to the GDNF receptor balances SPC growth with self-renewal.
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Affiliation(s)
- Robin M Hobbs
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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16
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Grisanti L, Falciatori I, Grasso M, Dovere L, Fera S, Muciaccia B, Fuso A, Berno V, Boitani C, Stefanini M, Vicini E. Identification of spermatogonial stem cell subsets by morphological analysis and prospective isolation. Stem Cells 2010; 27:3043-52. [PMID: 19711452 DOI: 10.1002/stem.206] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Spermatogenesis is maintained by a pool of spermatogonial stem cells (SSCs). Analyses of the molecular profile of SSCs have revealed the existence of subsets, indicating that the stem cell population is more heterogeneous than previously believed. However, SSC subsets are poorly characterized. In rodents, the first steps in spermatogenesis have been extensively investigated, both under physiological conditions and during the regenerative phase that follows germ cell damage. In the widely accepted model, the SSCs are type Asingle (As) spermatogonia. Here, we tested the hypothesis that As spermatogonia are phenotypically heterogeneous by analyzing glial cell line-derived neurotrophic factor (GDNF) family receptor alpha1 (GFRA1) expression in whole-mounted seminiferous tubules, via cytofluorimetric analysis and in vivo colonogenic assays. GFRA1 is a coreceptor for GDNF, a Sertoli cell-derived factor essential for SSC self-renewal and proliferation. Morphometric analysis demonstrated that 10% of As spermatogonia did not express GFRA1 but were colonogenic, as shown by germ cell transplantation assay. In contrast, cells selected for GFRA1 expression were not colonogenic in vivo. In human testes, GFRA1 was also heterogeneously expressed in Adark and in Apale spermatogonia, the earliest spermatogonia. In vivo 5-bromo-2'-deoxyuridine administration showed that both GFRA1(+) and GFRA1(-) As spermatogonia were engaged in the cell cycle, a finding supported by the lack of long-term label-retaining As spermatogonia. GFRA1 expression was asymmetric in 5% of paired cells, suggesting that As subsets may be generated by asymmetric cell division. Our data support the hypothesis of the existence of SSC subsets and reveal a previously unrecognized heterogeneity in the expression profile of As spermatogonia in vivo.
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Affiliation(s)
- Laura Grisanti
- Fondazione Pasteur Cenci Bolognetti, Department of Histology and Medical Embryology, and La Sapienza University of Rome, Rome, Italy
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17
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Wu Z, Falciatori I, Molyneux LA, Richardson TE, Chapman KM, Hamra FK. Spermatogonial culture medium: an effective and efficient nutrient mixture for culturing rat spermatogonial stem cells. Biol Reprod 2009; 81:77-86. [PMID: 19299316 DOI: 10.1095/biolreprod.108.072645] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
An economical and simplified procedure to derive and propagate fully functional lines of undifferentiated rat spermatogonia in vitro is presented. The procedure is based on the formulation of a new spermatogonial culture medium termed SG medium. The SG medium is composed of a 1:1 mixture of Dulbecco modified Eagle medium:Ham F12 nutrient, 20 ng/ml of GDNF, 25 ng/ml of FGF2, 100 microM 2-mercaptoethanol, 6 mM l-glutamine, and a 1x concentration of B27 Supplement Minus Vitamin A solution. Using SG medium, six individual spermatogonial lines were derived from the testes of six separate Sprague-Dawley rats. After proliferating over a 120-day period in SG medium, stem cells within the spermatogonial cultures effectively regenerated spermatogenesis in testes of busulfan-treated recipient rats, which transmitted the donor cell haplotype to more than 75% of progeny by natural breeding. Subculturing in SG medium did not require protease treatment and was achieved by passaging the loosely bound spermatogonial cultures at 1:3 dilutions onto fresh monolayers of irradiated DR4 mouse fibroblasts every 12 days. Spermatogonial lines derived and propagated using SG medium were characterized as homogeneous populations of ZBTB16(+) DAZL(+) cells endowed with spermatogonial stem cell potential.
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Affiliation(s)
- Zhuoru Wu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center in Dallas, Dallas, Texas 75390, USA
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18
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Kim J, Seandel M, Falciatori I, Wen D, Rafii S. CD34+ testicular stromal cells support long-term expansion of embryonic and adult stem and progenitor cells. Stem Cells 2008; 26:2516-22. [PMID: 18669907 DOI: 10.1634/stemcells.2008-0379] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Stem cells reside in specialized microenvironments created by supporting stromal cells that orchestrate self-renewal and lineage-specific differentiation. However, the precise identity of the cellular and molecular pathways that support self-renewal of stem cells is not known. For example, long-term culture of prototypical stem cells, such as adult spermatogonial stem and progenitor cells (SPCs), in vitro has been impeded by the lack of an optimal stromal cell line that initiates and sustains proliferation of these cells. Indeed, current methods, including the use of mouse embryonic fibroblasts (MEFs), have not been efficient and have generally led to inconsistent results. Here, we report the establishment of a novel CD34-positive cell line, referred to as JK1, derived from mouse testicular stromal cells that not only facilitated long-term SPC culture but also allowed faithful generation of SPCs and multipotent stem cells. SPCs generated on JK1 maintained key features of germ line stem cells, including expression of PLZF, DAZL, and GCNA. Furthermore, these feeders also promoted the long-term cultivation of other types of primitive cells including multipotent adult spermatogonial-derived stem cells, pluripotent murine embryonic stem cells, and embryonic germ cells derived from primordial germ cells. Stem cells could be passaged serially and still maintained expression of characteristic markers such as OCT4 and NANOG in vitro, as well as the ability to generate all three germ layers in vivo. These results indicate that the JK1 cell line is capable of promoting long-term culture of primitive cells. As such, this cell line allows for identification of stromal-derived factors that support long-term proliferation of various types of stem cells and constitutes a convenient alternative to other types of feeder layers. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Jiyeon Kim
- Department of Genetic Medicine, Howard Hughes Medical Institute, Ansary Center for Stem Cell Therapeutics, Weill Medical College of Cornell University, New York, New York 10065, USA
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Abstract
The undifferentiated spermatogonia of adult mouse testes are composed of both true stem cells and committed progenitors. It is unclear what normally prevents these adult germ cells from manifesting multipotency. The critical elements of the spermatogonial stem cell niche, while poorly understood, are thought to be composed of Sertoli cells with several other somatic cell types in close proximity. We recently discovered a novel orphan G-protein coupled receptor (GPR125) that is restricted to undifferentiated spermatogonia within the testis. GPR125 expression was maintained when the progenitor cells were extracted from the in vivo niche and propagated under growth conditions that recapitulate key elements of the niche. Such conditions preserved the ability of the cells to generate multipotent derivatives, known as multipotent adult spermatogonial derived progenitor cells (MASCs). Upon differentiation, the latter produced a variety tissues including functional endothelium, illustrating the potential applications of such cells. Thus, GPR125 represents a novel target for purifying adult stem and progenitors from tissues, with the goal of developing autologous multipotent cell lines.
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Affiliation(s)
- Marco Seandel
- Ansary Center for Stem Cell Therapeutics, Howard Hughes Medical Institute, Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
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20
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Seandel M, James D, Shmelkov SV, Falciatori I, Kim J, Chavala S, Scherr DS, Zhang F, Torres R, Gale NW, Yancopoulos GD, Murphy A, Valenzuela DM, Hobbs RM, Pandolfi PP, Rafii S. Generation of functional multipotent adult stem cells from GPR125+ germline progenitors. Nature 2007; 449:346-50. [PMID: 17882221 PMCID: PMC2935199 DOI: 10.1038/nature06129] [Citation(s) in RCA: 337] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 07/27/2007] [Indexed: 01/15/2023]
Abstract
Adult mammalian testis is a source of pluripotent stem cells. However, the lack of specific surface markers has hampered identification and tracking of the unrecognized subset of germ cells that gives rise to multipotent cells. Although embryonic-like cells can be derived from adult testis cultures after only several weeks in vitro, it is not known whether adult self-renewing spermatogonia in long-term culture can generate such stem cells as well. Here, we show that highly proliferative adult spermatogonial progenitor cells (SPCs) can be efficiently obtained by cultivation on mitotically inactivated testicular feeders containing CD34+ stromal cells. SPCs exhibit testicular repopulating activity in vivo and maintain the ability in long-term culture to give rise to multipotent adult spermatogonial-derived stem cells (MASCs). Furthermore, both SPCs and MASCs express GPR125, an orphan adhesion-type G-protein-coupled receptor. In knock-in mice bearing a GPR125-beta-galactosidase (LacZ) fusion protein under control of the native Gpr125 promoter (GPR125-LacZ), expression in the testis was detected exclusively in spermatogonia and not in differentiated germ cells. Primary GPR125-LacZ SPC lines retained GPR125 expression, underwent clonal expansion, maintained the phenotype of germline stem cells, and reconstituted spermatogenesis in busulphan-treated mice. Long-term cultures of GPR125+ SPCs (GSPCs) also converted into GPR125+ MASC colonies. GPR125+ MASCs generated derivatives of the three germ layers and contributed to chimaeric embryos, with concomitant downregulation of GPR125 during differentiation into GPR125- cells. MASCs also differentiated into contractile cardiac tissue in vitro and formed functional blood vessels in vivo. Molecular bookmarking by GPR125 in the adult mouse and, ultimately, in the human testis could enrich for a population of SPCs for derivation of GPR125+ MASCs, which may be employed for genetic manipulation, tissue regeneration and revascularization of ischaemic organs.
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Affiliation(s)
- Marco Seandel
- Howard Hughes Medical Institute, Department of Genetic Medicine, Weill Cornell Medical College, New York 10065, USA
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21
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Corallini S, Fera S, Grisanti L, Falciatori I, Muciaccia B, Stefanini M, Vicini E. Expression of the adaptor protein m-Numb in mouse male germ cells. Reproduction 2006; 132:887-97. [PMID: 17127749 DOI: 10.1530/rep-06-0062] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Numb is an adaptor protein that is asymmetrically inherited at mitosis and controls the fate of sibling cells in different species. The role of m-Numb (mammalian Numb) as an important cell fate-determining factor has extensively been described mostly in neural tissues, particularly in progenitor cells, in the mouse. Biochemical and genetic analyses have shown that Numb acts as an inhibitor of the Notch signaling pathway, an evolutionarily conserved pathway involved in the control of cell proliferation, differentiation, and apoptosis. In the present study, we sought to determine m-Numb distribution in germ cells in the postnatal mouse testis. We show that all four m-Numb isoforms are widely expressed during postnatal testis development. By reverse transcriptase-PCR and western blot analyses, we further identify p71 as the predominantly expressed isoform in germ cells. Moreover, we demonstrate through co-immunoprecipitation studies that m-Numb physically associates with Ap2a1, a component of the endocytotic clathrin-coated vesicles. Finally, we employed confocal immunofluorescence microscopy of whole mount seminiferous tubules and isolated germ cells to gain more insight into the subcellular localization of m-Numb. These morphological analyses confirmed m-Numb and Ap2a1 co-localization. However, we did not observe asymmetric localization of m-Numb neither in mitotic spermatogonial stem cells nor in more differentiated spermatogonial cells, suggesting that spermatogonial stem cell fate in the mouse does not rely on asymmetric partitioning of m-Numb.
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Affiliation(s)
- Serena Corallini
- Dipartimento di Istologia ed Embriologia Medica, Università di Roma La Sapienza, Via Antonio Scarpa 14, 00161 Rome, Italy
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Falciatori I, Borsellino G, Haliassos N, Boitani C, Corallini S, Battistini L, Bernardi G, Stefanini M, Vicini E. Identification and enrichment of spermatogonial stem cells displaying side-population phenotype in immature mouse testis. FASEB J 2003; 18:376-8. [PMID: 14688197 DOI: 10.1096/fj.03-0744fje] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In mammals, spermatogenesis is maintained by spermatogonial stem cells (SSC). In their niche, SSC divide to self-maintain and to produce a transit-amplifying population that eventually enters the meiotic cycle to give rise to spermatozoa. The low number of SSC and the lack of specific markers hinder their isolation and enrichment. Stem cells in several adult tissues can be identified by using their verapamil-sensitive Hoechst dye-effluxing properties, which define the characteristic "side population" (SP). Here we show, by multicolor flow cytometric analysis, that immature mouse testis contains a "side-population" (T-SP), which is Sca-1pos, Ep-CAMpos, EE2 pos, alpha6-integrin pos, and alpha(v)-integrin neg. A 13-fold enrichment in SSC activity was observed when sorted T-SP cells from ROSA 26 mice were transplanted in busulfan-treated mouse testis. Whereas an incomplete range of spermatogenic stages was encountered two months after transplantation of unsorted testicular cells, the transplantation of T-SP cells generated all associations of mouse germ cells representing the full range of spermatogenic stages. These data suggest that Hoechst staining and cell sorting might provide a novel approach to SSC enrichment in mammals.
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Affiliation(s)
- Ilaria Falciatori
- Department of Histology and Medical Embryology, University of Rome La Sapienza, Rome 00161, Italy
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Farioli-Vecchioli S, Nardacci R, Falciatori I, Stefanini S. Catalase immunocytochemistry allows automatic detection of lung type II alveolar cells. Histochem Cell Biol 2001; 115:333-9. [PMID: 11405062 DOI: 10.1007/s004180100259] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In mammalian lung, type II pneumocytes are especially critical in normal alveolar functioning, as they are the major source of surfactant and the progenitors of type I alveolar cells. Moreover, they undergo proliferation and transformation into type I cells in most types of cellular injury, where flattened type I pneumocytes are selectively destroyed. Hyperplasia of alveolar type II cells has also been described in some human chronic lung diseases. In lung, type II pneumocytes and non-ciliated bronchiolar cells are the unique cell types that contain a considerable amount of peroxisomes. Due to the presence of dihydroxyacetone phosphate acyltransferase and non-specific lipid-transfer protein, these organelles have been suggested to be involved in the synthesis and/or transport of the lipid moiety of surfactant. In the present research, the peroxisomal marker enzyme catalase was immunolocalised at the light microscopic level, utilising the avidin-biotin complex method, in lung specimens excised from newborn, adult and aged rats. In all the examined stages the immunoreactivity was so selective for type II pneumocytes it allowed quantitation of these cells by an automated detection system. This was accomplished on specimens from newborn rat lung, in which labelled alveolar cells were counted by a grey level-based procedure and their main morphometric parameters were determined.
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Affiliation(s)
- S Farioli-Vecchioli
- Department of Cellular and Developmental Biology, University of Rome La Sapienza, Piazzale Aldo Moro, 5, 00185 Rome, Italy
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