1
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Belicova L, Repnik U, Delpierre J, Gralinska E, Seifert S, Valenzuela JI, Morales-Navarrete HA, Franke C, Räägel H, Shcherbinina E, Prikazchikova T, Koteliansky V, Vingron M, Kalaidzidis YL, Zatsepin T, Zerial M. Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads. J Cell Biol 2021; 220:212522. [PMID: 34328499 PMCID: PMC8329733 DOI: 10.1083/jcb.202103003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Lumen morphogenesis results from the interplay between molecular pathways and mechanical forces. In several organs, epithelial cells share their apical surfaces to form a tubular lumen. In the liver, however, hepatocytes share the apical surface only between adjacent cells and form narrow lumina that grow anisotropically, generating a 3D network of bile canaliculi (BC). Here, by studying lumenogenesis in differentiating mouse hepatoblasts in vitro, we discovered that adjacent hepatocytes assemble a pattern of specific extensions of the apical membrane traversing the lumen and ensuring its anisotropic expansion. These previously unrecognized structures form a pattern, reminiscent of the bulkheads of boats, also present in the developing and adult liver. Silencing of Rab35 resulted in loss of apical bulkheads and lumen anisotropy, leading to cyst formation. Strikingly, we could reengineer hepatocyte polarity in embryonic liver tissue, converting BC into epithelial tubes. Our results suggest that apical bulkheads are cell-intrinsic anisotropic mechanical elements that determine the elongation of BC during liver tissue morphogenesis.
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Affiliation(s)
- Lenka Belicova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Urska Repnik
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julien Delpierre
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elzbieta Gralinska
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Christian Franke
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Helin Räägel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Nelson Laboratories LLC, Salt Lake City, UT
| | | | | | | | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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2
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Rybakova Y, Gonzalez JT, Bogorad R, Chauhan VP, Dong YL, Whittaker CA, Zatsepin T, Koteliansky V, Anderson DG. Identification of a long non-coding RNA regulator of liver carcinoma cell survival. Cell Death Dis 2021; 12:178. [PMID: 33589614 PMCID: PMC7884843 DOI: 10.1038/s41419-021-03453-w] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
Genomic studies have significantly improved our understanding of hepatocellular carcinoma (HCC) biology and have led to the discovery of multiple protein-coding genes driving hepatocarcinogenesis. In addition, these studies have identified thousands of new non-coding transcripts deregulated in HCC. We hypothesize that some of these transcripts may be involved in disease progression. Long non-coding RNAs are a large class of non-coding transcripts which participate in the regulation of virtually all cellular functions. However, a majority of lncRNAs remain dramatically understudied. Here, we applied a pooled shRNA-based screen to identify lncRNAs essential for HCC cell survival. We validated our screening results using RNAi, CRISPRi, and antisense oligonucleotides. We found a lncRNA, termed ASTILCS, that is critical for HCC cell growth and is overexpressed in tumors from HCC patients. We demonstrated that HCC cell death upon ASTILCS knockdown is associated with apoptosis induction and downregulation of a neighboring gene, protein tyrosine kinase 2 (PTK2), a crucial protein for HCC cell survival. Taken together, our study describes a new, non-coding RNA regulator of HCC.
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Affiliation(s)
- Yulia Rybakova
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - John T Gonzalez
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Roman Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Vikash P Chauhan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Yize L Dong
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | | | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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3
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Avalle L, Marino F, Camporeale A, Guglielmi C, Viavattene D, Bandini S, Conti L, Cimino J, Forni M, Zanini C, Ghigo A, Bogorad RL, Cavallo F, Provero P, Koteliansky V, Poli V. Liver-Specific siRNA-Mediated Stat3 or C3 Knockdown Improves the Outcome of Experimental Autoimmune Myocarditis. Mol Ther Methods Clin Dev 2020; 18:62-72. [PMID: 32577433 PMCID: PMC7301178 DOI: 10.1016/j.omtm.2020.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/19/2020] [Indexed: 11/15/2022]
Abstract
Myocarditis can lead to autoimmune disease, dilated cardiomyopathy, and heart failure, which is modeled in the mouse by cardiac myosin immunization (experimental autoimmune myocarditis [EAM]). Signal transducer and activator of transcription 3 (STAT3) systemic inhibition exerts both preventive and therapeutic effects in EAM, and STAT3 constitutive activation elicits immune-mediated myocarditis dependent on complement C3 and correlating with activation of the STAT3-interleukin 6 (IL-6) axis in the liver. Thus, liver-specific STAT3 inhibition may represent a therapeutic option, allowing to bypass the heart toxicity, predicted by systemic STAT3 inhibition. We therefore decided to explore the effectiveness of silencing liver Stat3 and C3 in preventing EAM onset and/or the recovery of cardiac functions. We first show that complement C3 and C5 genetic depletion significantly prevents the onset of spontaneous myocarditis, supporting the complement cascade as a viable target. In order to interfere with complement production and STAT3 activity specifically in the liver, we took advantage of liver-specific Stat3 or C3 small interfering (si)RNA nanoparticles, demonstrating that both siRNAs can significantly prevent myocarditis onset and improve the recovery of heart functions in EAM. Our data demonstrate that liver-specific Stat3/C3 siRNAs may represent a therapeutic option for autoimmune myocarditis and suggest that complement levels and activation might be predictive of progression to dilated cardiomyopathy.
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Affiliation(s)
- Lidia Avalle
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Francesca Marino
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Annalisa Camporeale
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Chiara Guglielmi
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Daniele Viavattene
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Silvio Bandini
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Laura Conti
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - James Cimino
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Marco Forni
- EuroClone S.p.A Research Laboratory, Molecular Biotechnology Center, University of Turin, Torino 10126, Italy
| | - Cristina Zanini
- EuroClone S.p.A Research Laboratory, Molecular Biotechnology Center, University of Turin, Torino 10126, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Roman L. Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Federica Cavallo
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow 121205, Russia
- Department of Chemistry, MV Lomonosov Moscow State University, Moscow 119991, Russia
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, Torino 10126, Italy
- Corresponding author Valeria Poli, Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy.
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4
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Smekalova EM, Gerashchenko MV, O'Connor PBF, Whittaker CA, Kauffman KJ, Fefilova AS, Zatsepin TS, Bogorad RL, Baranov PV, Langer R, Gladyshev VN, Anderson DG, Koteliansky V. In Vivo RNAi-Mediated eIF3m Knockdown Affects Ribosome Biogenesis and Transcription but Has Limited Impact on mRNA-Specific Translation. Mol Ther Nucleic Acids 2020; 19:252-266. [PMID: 31855834 PMCID: PMC6926209 DOI: 10.1016/j.omtn.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/20/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
Translation is an essential biological process, and dysregulation is associated with a range of diseases including ribosomopathies, diabetes, and cancer. Here, we examine translation dysregulation in vivo using RNAi to knock down the m-subunit of the translation initiation factor eIF3 in the mouse liver. Transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses show that eIF3m deficiency leads to the transcriptional response and changes in cellular translation that yield few detectable differences in the translation of particular mRNAs. The transcriptional response fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins) and cell metabolism (alterations in lipid, amino acid, nucleic acid, and drug metabolism). Analysis of ribosome biogenesis reveals inhibition of rRNA processing, highlighting decoupling of rRNA synthesis and ribosomal protein gene transcription in response to eIF3m knockdown. Interestingly, a similar reduction in eIF3m protein levels is associated with induction of the mTOR pathway in vitro but not in vivo. Overall, this work highlights the utility of a RNAi-based in vivo approach for studying the regulation of mammalian translation in vivo.
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Affiliation(s)
- Elena M Smekalova
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kevin J Kauffman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna S Fefilova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia; Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia.
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5
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Morales-Navarrete H, Nonaka H, Scholich A, Segovia-Miranda F, de Back W, Meyer K, Bogorad RL, Koteliansky V, Brusch L, Kalaidzidis Y, Jülicher F, Friedrich BM, Zerial M. Liquid-crystal organization of liver tissue. eLife 2019; 8:e44860. [PMID: 31204997 PMCID: PMC6598764 DOI: 10.7554/elife.44860] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Abstract
Functional tissue architecture originates by self-assembly of distinct cell types, following tissue-specific rules of cell-cell interactions. In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes. Since then, no significant progress has been made to derive the organizing principles of liver tissue. To solve this outstanding problem, we computationally reconstructed 3D tissue geometry from microscopy images of mouse liver tissue and analyzed it applying soft-condensed-matter-physics concepts. Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order. This does not depend exclusively on hepatocytes receiving instructive signals by endothelial cells, since silencing Integrin-β1 disrupted both liquid-crystal order and organization of the sinusoidal network. Our results suggest that bi-directional communication between hepatocytes and sinusoids underlies the self-organization of liver tissue.
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Affiliation(s)
| | - Hidenori Nonaka
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - André Scholich
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | | | - Walter de Back
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav CarusTechnische Universität DresdenDresdenGermany
- Centre for Information Services and High Performance ComputingTechnische Universität DresdenDresdenGermany
| | - Kirstin Meyer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeUnited States
| | - Victor Koteliansky
- Skolkovo Institute of Science and TechnologySkolkovoRussia
- Department of ChemistryMV Lomonosov Moscow State UniversityMoscowRussia
| | - Lutz Brusch
- Centre for Information Services and High Performance ComputingTechnische Universität DresdenDresdenGermany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
| | - Benjamin M Friedrich
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
- Center for Advancing Electronics DresdenTechnische Universität DresdenDresdenGermany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
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6
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Raven A, Lu WY, Man TY, Ferreira-Gonzalez S, O'Duibhir E, Dwyer BJ, Thomson JP, Meehan RR, Bogorad R, Koteliansky V, Kotelevtsev Y, Ffrench-Constant C, Boulter L, Forbes SJ. Corrigendum: Cholangiocytes act as facultative liver stem cells during impaired hepatocyte regeneration. Nature 2018; 555:402. [PMID: 29542689 DOI: 10.1038/nature25996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nature23015.
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7
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Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol 2018; 14:311-316. [PMID: 29377001 PMCID: PMC5902734 DOI: 10.1038/nchembio.2559] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [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: 10/05/2017] [Accepted: 12/11/2017] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 is a versatile RNA-guided genome editing tool. Here we demonstrate that partial replacement of RNA nucleotides with DNA nucleotides in CRISPR RNA (crRNA) enables efficient gene editing in human cells. This strategy of partial DNA replacement retains on-target activity when used with both crRNA and sgRNA, as well as with multiple guide sequences. Partial DNA replacement also works for crRNA of Cpf1, another CRISPR system. We find that partial DNA replacement in the guide sequence significantly reduces off-target genome editing through focused analysis of off-target cleavage, measurement of mismatch tolerance and genome-wide profiling of off-target sites. Using the structure of the Cas9-sgRNA complex as a guide, the majority of the 3' end of crRNA can be replaced with DNA nucleotide, and the 5 - and 3'-DNA-replaced crRNA enables efficient genome editing. Cas9 guided by a DNA-RNA chimera may provide a generalized strategy to reduce both the cost and the off-target genome editing in human cells.
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Affiliation(s)
- Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Sneha Suresh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Suet-Yan Kwan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Qiongqiong Wu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stephen Walsh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Junmei Ding
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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8
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Yin H, Song CQ, Suresh S, Wu Q, Walsh S, Rhym LH, Mintzer E, Bolukbasi MF, Zhu LJ, Kauffman K, Mou H, Oberholzer A, Ding J, Kwan SY, Bogorad RL, Zatsepin T, Koteliansky V, Wolfe SA, Xue W, Langer R, Anderson DG. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat Biotechnol 2017; 35:1179-1187. [PMID: 29131148 PMCID: PMC5901668 DOI: 10.1038/nbt.4005] [Citation(s) in RCA: 302] [Impact Index Per Article: 43.1] [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: 11/29/2016] [Accepted: 10/09/2017] [Indexed: 12/12/2022]
Abstract
Efficient genome editing with Cas9-sgRNA in vivo has required the use of viral delivery systems, which have limitations for clinical applications. Translational efforts to develop other RNA therapeutics have shown that judicious chemical modification of RNAs can improve therapeutic efficacy by reducing susceptibility to nuclease degradation. Guided by the structure of the Cas9-sgRNA complex, we identify regions of sgRNA that can be modified while maintaining or enhancing genome-editing activity, and we develop an optimal set of chemical modifications for in vivo applications. Using lipid nanoparticle formulations of these enhanced sgRNAs (e-sgRNA) and mRNA encoding Cas9, we show that a single intravenous injection into mice induces >80% editing of Pcsk9 in the liver. Serum Pcsk9 is reduced to undetectable levels, and cholesterol levels are significantly lowered about 35% to 40% in animals. This strategy may enable non-viral, Cas9-based genome editing in the liver in clinical settings.
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Affiliation(s)
- Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Sneha Suresh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Qiongqiong Wu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stephen Walsh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Luke Hyunsik Rhym
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Mehmet Fatih Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kevin Kauffman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Alicia Oberholzer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Junmei Ding
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Suet-Yan Kwan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Timofei Zatsepin
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Victor Koteliansky
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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9
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Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S. Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration. Dev Cell 2017; 42:616-625.e8. [PMID: 28890072 DOI: 10.1016/j.devcel.2017.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/16/2017] [Accepted: 07/26/2017] [Indexed: 01/20/2023]
Abstract
The liver is the only organ in mammals that fully regenerates even after major injury. To identify orchestrators of this regenerative response, we performed quantitative large-scale proteomics analysis of cytoplasmic and nuclear fractions from normal versus regenerating mouse liver. Proteins of the ubiquitin-proteasome pathway were rapidly upregulated after two-third hepatectomy, with the ubiquitin ligase Nedd4-1 being a top hit. In vivo knockdown of Nedd4-1 in hepatocytes through nanoparticle-mediated delivery of small interfering RNA caused severe liver damage and inhibition of cell proliferation after hepatectomy, resulting in liver failure. Mechanistically, we demonstrate that Nedd4-1 is required for efficient internalization of major growth factor receptors involved in liver regeneration and their downstream mitogenic signaling. These results highlight the power of large-scale proteomics to identify key players in liver regeneration and the importance of posttranslational regulation of growth factor signaling in this process. Finally, they identify an essential function of Nedd4-1 in tissue repair.
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Affiliation(s)
- Marc Bachofner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Speicher
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Division of Health Science Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sukalp Muzumdar
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Carina P Derrer
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Fabrizio Hürlimann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Friederike Böhm
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zürich, University of Zürich/ETH Zürich, 8057 Zürich, Switzerland
| | - Tobias Kockmann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland; Functional Genomics Center Zürich, University of Zürich/ETH Zürich, 8057 Zürich, Switzerland
| | - Ekaterina Kachaylo
- Swiss HPB Center, Division of Visceral and Transplantation Surgery, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Michael Meyer
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Susagna Padrissa-Altés
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Rolf Graf
- Swiss HPB Center, Division of Visceral and Transplantation Surgery, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Division of Health Science Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Health Science Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, ul. Novaya, d.100, Skolkovo 143025, Russian Federation
| | - Ulrich Auf dem Keller
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland.
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10
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Smekalova EM, Kotelevtsev YV, Leboeuf D, Shcherbinina EY, Fefilova AS, Zatsepin TS, Koteliansky V. lncRNA in the liver: Prospects for fundamental research and therapy by RNA interference. Biochimie 2016; 131:159-172. [DOI: 10.1016/j.biochi.2016.06.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/14/2016] [Indexed: 12/19/2022]
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11
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Majouga A, Ivanenkov Y, Veselov M, Lopuhov A, Maklakova S, Beloglazkina E, Binevski P, Klyachko N, Sandulenko Y, Galkina N, Koteliansky V. Identification of Novel Small-Molecule ASGP-R Ligands. Curr Drug Deliv 2016; 13:1303-1312. [DOI: 10.2174/1567201813666160719144651] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/22/2016] [Accepted: 06/19/2016] [Indexed: 11/22/2022]
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12
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Abstract
This review covers the basic aspects of small interfering RNA delivery by lipid nano-particles (LNPs) and elaborates on the current status of clinical trials for these systems. We briefly describe the roles of all LNP components and possible strategies for their improvement. We also focus on the current clinical trials using LNP-formulated RNA and the possible outcomes for therapy in the near future. Also, we present a critical analysis of selected clinical trials that reveals the common logic behind target selection. We address this review to a wide audience, especially to medical doctors who are interested in the application of RNA interference-based treatment platforms. We anticipate that this review may spark interest in this particular audience and generate new ideas in target selection for the disorders they are dealing with.
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Affiliation(s)
- Timofei S Zatsepin
- Center of Functional Genomics, Skolkovo Institute of Science and Technology; Department of Chemistry, Lomonosov Moscow State University; Production Department, Central Research Institute of Epidemiology, Moscow, Russia
| | - Yuri V Kotelevtsev
- Center of Functional Genomics, Skolkovo Institute of Science and Technology
| | - Victor Koteliansky
- Center of Functional Genomics, Skolkovo Institute of Science and Technology; Department of Chemistry, Lomonosov Moscow State University
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13
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Yin H, Bogorad RL, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, Zerial M, Langer R, Anderson DG, Koteliansky V. RNAi-nanoparticulate manipulation of gene expression as a new functional genomics tool in the liver. J Hepatol 2016; 64:899-907. [PMID: 26658687 PMCID: PMC5381270 DOI: 10.1016/j.jhep.2015.11.028] [Citation(s) in RCA: 8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/22/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS The Hippo pathway controls organ size through a negative regulation of the transcription co-activator Yap1. The overexpression of hyperactive mutant Yap1 or deletion of key components in the Hippo pathway leads to increased organ size in different species. Analysis of interactions of this pathway with other cellular signals corroborating organ size control is limited in part due to the difficulties associated with development of rodent models. METHODS Here, we develop a new model of reversible induction of the liver size in mice using siRNA-nanoparticles targeting two kinases of the Hippo pathway, namely, mammalian Ste20 family kinases 1 and 2 (Mst1 and Mst2), and an upstream regulator, neurofibromatosis type II (Nf2). RESULTS The triple siRNAs nanoparticle-induced hepatomegaly in mice phenocopies one observed with Mst1(-/-)Mst2(-/-) liver-specific depletion, as shown by extensive proliferation of hepatocytes and activation of Yap1. The simultaneous co-treatment with a fourth siRNA nanoparticle against Yap1 fully blocked the liver growth. Hippo pathway-induced liver enlargement is associated with p53 activation, evidenced by its accumulation in the nuclei and upregulation of its target genes. Moreover, injections of the triple siRNAs nanoparticle in p53(LSL/LSL) mice shows that livers lacking p53 expression grow faster and exceed the size of livers in p53 wild-type animals, indicating a role of p53 in controlling Yap1-induced liver growth. CONCLUSION Our data show that siRNA-nanoparticulate manipulation of gene expression can provide the reversible control of organ size in adult animals, which presents a new avenue for the investigation of complex regulatory networks in liver.
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Affiliation(s)
- Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Stephen Walsh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Iris Zhuang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hidenori Nonaka
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden 01307, Germany
| | - Vera Ruda
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | - Wen Xue
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden 01307, Germany
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 119991, Russia.
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14
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Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, Xue W, Anderson DG. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol 2016; 34:328-33. [PMID: 26829318 PMCID: PMC5423356 DOI: 10.1038/nbt.3471] [Citation(s) in RCA: 621] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/05/2016] [Indexed: 12/15/2022]
Abstract
The combination of Cas9, guide RNA and repair template DNA can induce
precise gene editing and the correction of genetic diseases in adult mammals.
However, clinical implementation of this technology requires safe and effective
delivery of all of these components into the nuclei of the target tissue. Here,
we combine lipid nanoparticle–mediated delivery of Cas9 mRNA with
adeno-associated viruses encoding a sgRNA and a repair template to induce repair
of a disease gene in adult animals. We applied our delivery strategy to a mouse
model of human hereditary tyrosinemia and show that the treatment generated
fumarylacetoacetate hydrolase (Fah)-positive hepatocytes by correcting the
causative Fah-splicing mutation. Treatment rescued disease symptoms such as
weight loss and liver damage. The efficiency of correction was
>6% of hepatocytes after a single application, suggesting
potential utility of Cas9-based therapeutic genome editing for a range of
diseases.
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Affiliation(s)
- Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Joseph R Dorkin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lihua J Zhu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yingxiang Li
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P.R. China
| | - Qiongqiong Wu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Angela Park
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Junghoon Yang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sneha Suresh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aizhan Bizhanova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Mehmet F Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Stephen Walsh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Guangping Gao
- Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yizhou Dong
- College of Pharmacy, the Ohio State University, Columbus, Ohio, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, Russia
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences &Technology, Cambridge, Massachusetts, USA.,Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences &Technology, Cambridge, Massachusetts, USA.,Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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15
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Padrissa-Altés S, Bachofner M, Bogorad RL, Pohlmeier L, Rossolini T, Böhm F, Liebisch G, Hellerbrand C, Koteliansky V, Speicher T, Werner S. Control of hepatocyte proliferation and survival by Fgf receptors is essential for liver regeneration in mice. Gut 2015; 64:1444-53. [PMID: 25416068 DOI: 10.1136/gutjnl-2014-307874] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Fibroblast growth factors (Fgfs) are key orchestrators of development, and a role of Fgfs in tissue repair is emerging. Here we studied the consequences of inducible loss of Fgf receptor (Fgfr) 4, the major Fgf receptor (Fgfr) on hepatocytes, alone or in combination with Fgfr1 and Fgfr2, for liver regeneration after PH. DESIGN We used siRNA delivered via nanoparticles combined with liver-specific gene knockout to study Fgfr function in liver regeneration. Liver or blood samples were analysed using histology, immunohistochemistry,real-time RT-PCR, western blotting and ELISA. RESULTS siRNA-mediated knockdown of Fgfr4 severely affected liver regeneration due to impairment of hepatocyte proliferation combined with liver necrosis.Mechanistically, the proliferation defect resulted from inhibition of an Fgf15-Fgfr4-Stat3 signalling pathway,which is required for injury-induced expression of the Foxm1 transcription factor and subsequent cell cycle progression, while elevated levels of intrahepatic toxicbile acids were identified as the likely cause of the necrotic damage. Failure of liver mass restoration in Fgfr4 knockdown mice was prevented at least in part by compensatory hypertrophy of hepatocytes. Most importantly, our data revealed partially redundant functions of Fgf receptors in the liver, since knock down of Fgfr4 in mice lacking Fgfr1 and Fgfr2 in hepatocytes caused liver failure after PH due to severe liver necrosis and a defect in regeneration. CONCLUSIONS These results demonstrate that Fgfr signalling in hepatocytes is essential for liver regeneration and suggest activation of Fgfr signalling asa promising approach for the improvement of the liver's regenerative capacity.
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MESH Headings
- Animals
- Blotting, Western
- Cell Proliferation
- Cell Survival
- Cells, Cultured
- Cytokines/metabolism
- Disease Models, Animal
- Enzyme-Linked Immunosorbent Assay
- Hepatectomy/methods
- Hepatocytes/metabolism
- Hepatocytes/physiology
- Immunohistochemistry
- Liver/pathology
- Liver Regeneration/physiology
- Male
- Mice
- Mice, Knockout
- RNA, Small Interfering/analysis
- Real-Time Polymerase Chain Reaction/methods
- Receptor, Fibroblast Growth Factor, Type 4/genetics
- Receptor, Fibroblast Growth Factor, Type 4/metabolism
- Signal Transduction
- Statistics, Nonparametric
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16
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Gilleron J, Paramasivam P, Zeigerer A, Querbes W, Marsico G, Andree C, Seifert S, Amaya P, Stöter M, Koteliansky V, Waldmann H, Fitzgerald K, Kalaidzidis Y, Akinc A, Maier MA, Manoharan M, Bickle M, Zerial M. Identification of siRNA delivery enhancers by a chemical library screen. Nucleic Acids Res 2015. [PMID: 26220182 PMCID: PMC4652771 DOI: 10.1093/nar/gkv762] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [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] [Indexed: 12/21/2022] Open
Abstract
Most delivery systems for small interfering RNA therapeutics depend on endocytosis and release from endo-lysosomal compartments. One approach to improve delivery is to identify small molecules enhancing these steps. It is unclear to what extent such enhancers can be universally applied to different delivery systems and cell types. Here, we performed a compound library screen on two well-established siRNA delivery systems, lipid nanoparticles and cholesterol conjugated-siRNAs. We identified fifty-one enhancers improving gene silencing 2–5 fold. Strikingly, most enhancers displayed specificity for one delivery system only. By a combination of quantitative fluorescence and electron microscopy we found that the enhancers substantially differed in their mechanism of action, increasing either endocytic uptake or release of siRNAs from endosomes. Furthermore, they acted either on the delivery system itself or the cell, by modulating the endocytic system via distinct mechanisms. Interestingly, several compounds displayed activity on different cell types. As proof of principle, we showed that one compound enhanced siRNA delivery in primary endothelial cells in vitro and in the endocardium in the mouse heart. This study suggests that a pharmacological approach can improve the delivery of siRNAs in a system-specific fashion, by exploiting distinct mechanisms and acting upon multiple cell types.
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Affiliation(s)
- Jerome Gilleron
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Nice, France; Université de Nice Sophia-Antipolis, Nice, France
| | - Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Anja Zeigerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | | | - Giovanni Marsico
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Cordula Andree
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Pablo Amaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Victor Koteliansky
- Lomonosov Moscow State University, Chemistry Department, Leninskie Gory, 1/3, Moscow 119991, Russia Skolkovo Institute of Science and Technology, 100 Novaya str., Skolkovo, Odinsovsky district, Moscow 143025, Russia
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | | | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108 01307, Dresden, Germany
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17
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Zeigerer A, Bogorad RL, Sharma K, Gilleron J, Seifert S, Sales S, Berndt N, Bulik S, Marsico G, D'Souza RCJ, Lakshmanaperumal N, Meganathan K, Natarajan K, Sachinidis A, Dahl A, Holzhütter HG, Shevchenko A, Mann M, Koteliansky V, Zerial M. Regulation of liver metabolism by the endosomal GTPase Rab5. Cell Rep 2015; 11:884-892. [PMID: 25937276 DOI: 10.1016/j.celrep.2015.04.018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 02/24/2015] [Accepted: 04/07/2015] [Indexed: 11/28/2022] Open
Abstract
The liver maintains glucose and lipid homeostasis by adapting its metabolic activity to the energy needs of the organism. Communication between hepatocytes and extracellular environment via endocytosis is key to such homeostasis. Here, we addressed the question of whether endosomes are required for gluconeogenic gene expression. We took advantage of the loss of endosomes in the mouse liver upon Rab5 silencing. Strikingly, we found hepatomegaly and severe metabolic defects such as hypoglycemia, hypercholesterolemia, hyperlipidemia, and glycogen accumulation that phenocopied those found in von Gierke's disease, a glucose-6-phosphatase (G6Pase) deficiency. G6Pase deficiency alone can account for the reduction in hepatic glucose output and glycogen accumulation as determined by mathematical modeling. Interestingly, we uncovered functional alterations in the transcription factors, which regulate G6Pase expression. Our data highlight a requirement of Rab5 and the endosomal system for the regulation of gluconeogenic gene expression that has important implications for metabolic diseases.
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Affiliation(s)
- Anja Zeigerer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Kirti Sharma
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jerome Gilleron
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Université de Nice Sophia-Antipolis, 06108 Nice, France
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Sascha Bulik
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Giovanni Marsico
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Rochelle C J D'Souza
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Kesavan Meganathan
- University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Karthick Natarajan
- University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Agapios Sachinidis
- University of Cologne, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB655, BIOTEC, Technical University Dresden, 01307 Dresden, Germany
| | | | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, ul. Novaya, d.100, Skolkovo 143025, Russian Federation; Lomonosov Moscow State University, Chemistry Department, Leninskie, Gory, 1/3, Moscow 119991, Russian Federation
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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18
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Herr KJ, Tsang YHN, Ong JWE, Li Q, Yap LL, Yu W, Yin H, Bogorad RL, Dahlman JE, Chan YG, Bay BH, Singaraja R, Anderson DG, Koteliansky V, Viasnoff V, Thiery JP. Loss of α-catenin elicits a cholestatic response and impairs liver regeneration. Sci Rep 2014; 4:6835. [PMID: 25355493 PMCID: PMC4213774 DOI: 10.1038/srep06835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/10/2014] [Indexed: 12/25/2022] Open
Abstract
The liver is unique in its capacity to regenerate after injury, during which hepatocytes actively divide and establish cell-cell contacts through cell adhesion complexes. Here, we demonstrate that the loss of α-catenin, a well-established adhesion component, dramatically disrupts liver regeneration. Using a partial hepatectomy model, we show that regenerated livers from α-catenin knockdown mice are grossly larger than control regenerated livers, with an increase in cell size and proliferation. This increased proliferation correlated with increased YAP activation, implicating α-catenin in the Hippo/YAP pathway. Additionally, α-catenin knockdown mice exhibited a phenotype reminiscent of clinical cholestasis, with drastically altered bile canaliculi, elevated levels of bile components and signs of jaundice and inflammation. The disrupted regenerative capacity is a result of actin cytoskeletal disorganisation, leading to a loss of apical microvilli, dilated lumens in the bile canaliculi, and leaky tight junctions. This study illuminates a novel, essential role for α-catenin in liver regeneration.
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Affiliation(s)
- Keira Joann Herr
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Ying-hung Nicole Tsang
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Joanne Wei En Ong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Qiushi Li
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Lai Lai Yap
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Hao Yin
- Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A
| | - Roman L Bogorad
- Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A
| | - James E Dahlman
- 1] Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A [2] Department of Biology, MIT, Massachusetts, U.S.A [3] Institute for Medical Engineering and Science, MIT, Massachusetts, U.S.A
| | - Yee Gek Chan
- Department of Anatomy, National University of Singapore, Singapore
| | - Boon Huat Bay
- Department of Anatomy, National University of Singapore, Singapore
| | - Roshni Singaraja
- Translational Laboratory in Genetic Medicine, A*STAR, Singapore, Singapore
| | - Daniel G Anderson
- 1] Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A [2] Institute for Medical Engineering and Science, MIT, Massachusetts, U.S.A [3] Department of Chemical Engineering, MIT, Massachusetts, U.S.A [4] Department of Anaesthesiology, Children's Hospital Boston, Harvard Medical School, Massachusetts, U.S.A
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology ul, Skolkovo, Russian Federation
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Jean Paul Thiery
- 1] Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore [2] Department of Biochemistry School of Medicine National University of Singapore, Singapore [3] Cancer Science Institute National University of Singapore, Singapore
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19
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Ruda VM, Chandwani R, Sehgal A, Bogorad RL, Akinc A, Charisse K, Tarakhovsky A, Novobrantseva TI, Koteliansky V. The roles of individual mammalian argonautes in RNA interference in vivo. PLoS One 2014; 9:e101749. [PMID: 24992693 PMCID: PMC4081796 DOI: 10.1371/journal.pone.0101749] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 12/17/2013] [Accepted: 05/28/2014] [Indexed: 11/26/2022] Open
Abstract
Argonaute 2 (Ago2) is the only mammalian Ago protein capable of mRNA cleavage. It has been reported that the activity of the short interfering RNA targeting coding sequence (CDS), but not 3′ untranslated region (3′UTR) of an mRNA, is solely dependent on Ago2 in vitro. These studies utilized extremely high doses of siRNAs and overexpressed Ago proteins, as well as were directed at various highly expressed reporter transgenes. Here we report the effect of Ago2 in vivo on targeted knockdown of several endogenous genes by siRNAs, targeting both CDS and 3′UTR. We show that siRNAs targeting CDS lose their activity in the absence of Ago2, whereas both Ago1 and Ago3 proteins contribute to residual 3′UTR-targeted siRNA-mediated knockdown observed in the absence of Ago2 in mouse liver. Our results provide mechanistic insight into two components mediating RNAi under physiological conditions: mRNA cleavage dependent and independent. In addition our results contribute a novel consideration for designing most efficacious siRNA molecules with the preference given to 3′UTR targeting as to harness the activity of several Ago proteins.
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Affiliation(s)
- Vera M. Ruda
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (VMR); (VK)
| | - Rohit Chandwani
- Laboratory of Immune Cell Epigenetics and Signaling, Rockefeller University, New York, New York, United States of America
| | - Alfica Sehgal
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Roman L. Bogorad
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Klaus Charisse
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, Rockefeller University, New York, New York, United States of America
| | | | - Victor Koteliansky
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (VMR); (VK)
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20
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Leuschner F, Courties G, Dutta P, Mortensen LJ, Gorbatov R, Sena B, Novobrantseva TI, Borodovsky A, Fitzgerald K, Koteliansky V, Iwamoto Y, Bohlender M, Meyer S, Lasitschka F, Meder B, Katus HA, Lin C, Libby P, Swirski FK, Anderson DG, Weissleder R, Nahrendorf M. Silencing of CCR2 in myocarditis. Eur Heart J 2014; 36:1478-88. [PMID: 24950695 DOI: 10.1093/eurheartj/ehu225] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 05/13/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Myocarditis is characterized by inflammatory cell infiltration of the heart and subsequent deterioration of cardiac function. Monocytes are the most prominent population of accumulating leucocytes. We investigated whether in vivo administration of nanoparticle-encapsulated siRNA targeting chemokine (C-C motif) receptor 2 (CCR2)-a chemokine receptor crucial for leucocyte migration in humans and mice--reduces inflammation in autoimmune myocarditis. METHODS AND RESULTS In myocardium of patients with myocarditis, CCL2 mRNA levels and CCR2(+) cells increased (P < 0.05), motivating us to pursue CCR2 silencing. Flow cytometric analysis showed that siRNA silencing of CCR2 (siCCR2) reduced the number of Ly6C(high) monocytes in hearts of mice with acute autoimmune myocarditis by 69% (P < 0.05), corroborated by histological assessment. The nanoparticle-delivered siRNA was not only active in monocytes but also in bone marrow haematopoietic progenitor cells. Treatment with siCCR2 reduced the migration of bone marrow granulocyte macrophage progenitors into the blood. Cellular magnetic resonance imaging (MRI) after injection of macrophage-avid magnetic nanoparticles detected myocarditis and therapeutic effects of RNAi non-invasively. Mice with acute myocarditis showed enhanced macrophage MRI contrast, which was prevented by siCCR2 (P < 0.05). Follow-up MRI volumetry revealed that siCCR2 treatment improved ejection fraction (P < 0.05 vs. control siRNA-treated mice). CONCLUSION This study highlights the importance of CCR2 in the pathogenesis of myocarditis. In addition, we show that siCCR2 affects leucocyte progenitor trafficking. The data also point to a novel therapeutic strategy for the treatment of myocarditis.
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Affiliation(s)
- Florian Leuschner
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA Department of Cardiology, Medical University Hospital Heidelberg, Im Neuenheimer Feld 410, Heidelberg D-69120, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Gabriel Courties
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Partha Dutta
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Luke J Mortensen
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Rostic Gorbatov
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Brena Sena
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | | | - Anna Borodovsky
- Alnylam Pharmaceuticals, 300 3rd Street, Cambridge, MA 02142, USA
| | - Kevin Fitzgerald
- Alnylam Pharmaceuticals, 300 3rd Street, Cambridge, MA 02142, USA
| | - Victor Koteliansky
- Department of Chemical Engineering, Massachusetts Institute of Technology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yoshiko Iwamoto
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Marina Bohlender
- Department of Cardiology, Medical University Hospital Heidelberg, Im Neuenheimer Feld 410, Heidelberg D-69120, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Soeren Meyer
- Department of Cardiology, Medical University Hospital Heidelberg, Im Neuenheimer Feld 410, Heidelberg D-69120, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 220/221, Heidelberg 69120, Germany
| | - Benjamin Meder
- Department of Cardiology, Medical University Hospital Heidelberg, Im Neuenheimer Feld 410, Heidelberg D-69120, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Hugo A Katus
- Department of Cardiology, Medical University Hospital Heidelberg, Im Neuenheimer Feld 410, Heidelberg D-69120, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Charles Lin
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Peter Libby
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Filip K Swirski
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, University Hospital Heidelberg, Heidelberg, Germany David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Division of Health Science Technology, Massachusetts Institute of Technology, Boston, MA, USA Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Matthias Nahrendorf
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA
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21
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Speicher T, Siegenthaler B, Bogorad RL, Ruppert R, Petzold T, Padrissa-Altes S, Bachofner M, Anderson DG, Koteliansky V, Fässler R, Werner S. Knockdown and knockout of β1-integrin in hepatocytes impairs liver regeneration through inhibition of growth factor signalling. Nat Commun 2014; 5:3862. [PMID: 24844558 DOI: 10.1038/ncomms4862] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/11/2014] [Indexed: 02/06/2023] Open
Abstract
The liver has a unique regenerative capability, which involves extensive remodelling of cell-cell and cell-matrix contacts. Here we study the role of integrins in mouse liver regeneration using Cre/loxP-mediated gene deletion or intravenous delivery of β1-integrin siRNA formulated into nanoparticles that predominantly target hepatocytes. We show that although short-term loss of β1-integrin has no obvious consequences for normal livers, partial hepatectomy leads to severe liver necrosis and reduced hepatocyte proliferation. Mechanistically, loss of β1-integrin in hepatocytes impairs ligand-induced phosphorylation of the epidermal growth factor and hepatocyte growth factor receptors, thereby attenuating downstream receptor signalling in vitro and in vivo. These results identify a crucial role and novel mechanism of action of β1-integrins in liver regeneration and demonstrate that protein depletion by nanoparticle-based delivery of specific siRNA is a powerful strategy to study gene function in the regenerating liver.
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Affiliation(s)
- Tobias Speicher
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich,8093, Switzerland
| | - Beat Siegenthaler
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich,8093, Switzerland
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Raphael Ruppert
- Department of Molecular Medicine, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Tobias Petzold
- Department of Molecular Medicine, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Susagna Padrissa-Altes
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich,8093, Switzerland
| | - Marc Bachofner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich,8093, Switzerland
| | - Daniel G Anderson
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Division of Health Science Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, ul. Novaya, d.100, Skolkovo 143025, Russian Federation
| | - Reinhard Fässler
- Department of Molecular Medicine, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich,8093, Switzerland
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22
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Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol 2014; 32:551-3. [PMID: 24681508 DOI: 10.1038/nbt.2884] [Citation(s) in RCA: 671] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/20/2014] [Indexed: 02/07/2023]
Abstract
We demonstrate CRISPR-Cas9-mediated correction of a Fah mutation in hepatocytes in a mouse model of the human disease hereditary tyrosinemia. Delivery of components of the CRISPR-Cas9 system by hydrodynamic injection resulted in initial expression of the wild-type Fah protein in ∼1/250 liver cells. Expansion of Fah-positive hepatocytes rescued the body weight loss phenotype. Our study indicates that CRISPR-Cas9-mediated genome editing is possible in adult animals and has potential for correction of human genetic diseases.
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Affiliation(s)
- Hao Yin
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2]
| | - Wen Xue
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2]
| | - Sidi Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eric Benedetti
- Oregon Stem Cell Center, Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Markus Grompe
- Oregon Stem Cell Center, Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Phillip A Sharp
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tyler Jacks
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel G Anderson
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts, USA. [4] Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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23
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Csordás G, Golenár T, Seifert EL, Kamer KJ, Sancak Y, Perocchi F, Moffat C, Weaver D, Perez SDLF, Bogorad R, Koteliansky V, Adijanto J, Mootha VK, Hajnóczky G. MICU1 controls both the threshold and cooperative activation of the mitochondrial Ca²⁺ uniporter. Cell Metab 2013; 17:976-987. [PMID: 23747253 PMCID: PMC3722067 DOI: 10.1016/j.cmet.2013.04.020] [Citation(s) in RCA: 365] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/02/2013] [Accepted: 04/26/2013] [Indexed: 12/18/2022]
Abstract
Mitochondrial Ca(2+) uptake via the uniporter is central to cell metabolism, signaling, and survival. Recent studies identified MCU as the uniporter's likely pore and MICU1, an EF-hand protein, as its critical regulator. How this complex decodes dynamic cytoplasmic [Ca(2+)] ([Ca(2+)]c) signals, to tune out small [Ca(2+)]c increases yet permit pulse transmission, remains unknown. We report that loss of MICU1 in mouse liver and cultured cells causes mitochondrial Ca(2+) accumulation during small [Ca(2+)]c elevations but an attenuated response to agonist-induced [Ca(2+)]c pulses. The latter reflects loss of positive cooperativity, likely via the EF-hands. MICU1 faces the intermembrane space and responds to [Ca(2+)]c changes. Prolonged MICU1 loss leads to an adaptive increase in matrix Ca(2+) binding, yet cells show impaired oxidative metabolism and sensitization to Ca(2+) overload. Collectively, the data indicate that MICU1 senses the [Ca(2+)]c to establish the uniporter's threshold and gain, thereby allowing mitochondria to properly decode different inputs.
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Affiliation(s)
- György Csordás
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tünde Golenár
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Erin L Seifert
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Kimberli J Kamer
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yasemin Sancak
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School and Broad Institute, Cambridge, MA 02142, USA
| | - Fabiana Perocchi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School and Broad Institute, Cambridge, MA 02142, USA; Gene Center, Ludwig-Maximilians-Universität, Munich D-81377, Germany
| | - Cynthia Moffat
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - David Weaver
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sergio de la Fuente Perez
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Roman Bogorad
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Jeffrey Adijanto
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School and Broad Institute, Cambridge, MA 02142, USA.
| | - György Hajnóczky
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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24
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Plovanich M, Bogorad RL, Sancak Y, Kamer KJ, Strittmatter L, Li AA, Girgis HS, Kuchimanchi S, De Groot J, Speciner L, Taneja N, OShea J, Koteliansky V, Mootha VK. MICU2, a paralog of MICU1, resides within the mitochondrial uniporter complex to regulate calcium handling. PLoS One 2013; 8:e55785. [PMID: 23409044 PMCID: PMC3567112 DOI: 10.1371/journal.pone.0055785] [Citation(s) in RCA: 344] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 12/31/2012] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial calcium uptake is present in nearly all vertebrate tissues and is believed to be critical in shaping calcium signaling, regulating ATP synthesis and controlling cell death. Calcium uptake occurs through a channel called the uniporter that resides in the inner mitochondrial membrane. Recently, we used comparative genomics to identify MICU1 and MCU as the key regulatory and putative pore-forming subunits of this channel, respectively. Using bioinformatics, we now report that the human genome encodes two additional paralogs of MICU1, which we call MICU2 and MICU3, each of which likely arose by gene duplication and exhibits distinct patterns of organ expression. We demonstrate that MICU1 and MICU2 are expressed in HeLa and HEK293T cells, and provide multiple lines of biochemical evidence that MCU, MICU1 and MICU2 reside within a complex and cross-stabilize each other's protein expression in a cell-type dependent manner. Using in vivo RNAi technology to silence MICU1, MICU2 or both proteins in mouse liver, we observe an additive impairment in calcium handling without adversely impacting mitochondrial respiration or membrane potential. The results identify MICU2 as a new component of the uniporter complex that may contribute to the tissue-specific regulation of this channel.
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Affiliation(s)
- Molly Plovanich
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Roman L. Bogorad
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yasemin Sancak
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Kimberli J. Kamer
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Laura Strittmatter
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Andrew A. Li
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Hany S. Girgis
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Satya Kuchimanchi
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Jack De Groot
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Lauren Speciner
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Nathan Taneja
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Jonathan OShea
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Victor Koteliansky
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vamsi K. Mootha
- Departments of Molecular Biology and Medicine, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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25
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Csordás G, Seifert EL, Golenár T, Moffat C, de la Fuente Perez S, Weaver D, Bogorad R, Koteliansky V, Mootha VK, Hajnóczky G. MICU1-dependent Threshold and Cooperativity of Mitochondrial Ca2+ Uptake in the Liver. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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So JS, Hur KY, Tarrio M, Ruda V, Frank-Kamenetsky M, Fitzgerald K, Koteliansky V, Lichtman AH, Iwawaki T, Glimcher LH, Lee AH. Silencing of lipid metabolism genes through IRE1α-mediated mRNA decay lowers plasma lipids in mice. Cell Metab 2012; 16:487-99. [PMID: 23040070 PMCID: PMC3475419 DOI: 10.1016/j.cmet.2012.09.004] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/29/2012] [Accepted: 09/10/2012] [Indexed: 12/14/2022]
Abstract
XBP1 is a key regulator of the unfolded protein response (UPR), which is involved in a wide range of physiological and pathological processes. XBP1 ablation in liver causes profound hypolipidemia in mice, highlighting its critical role in lipid metabolism. XBP1 deficiency triggers feedback activation of its upstream enzyme IRE1α, instigating regulated IRE1-dependent decay (RIDD) of cytosolic mRNAs. Here, we identify RIDD as a crucial control mechanism of lipid homeostasis. Suppression of RIDD by RNA interference or genetic ablation of IRE1α reversed hypolipidemia in XBP1-deficient mice. Comprehensive microarray analysis of XBP1 and/or IRE1α-deficient liver identified genes involved in lipogenesis and lipoprotein metabolism as RIDD substrates, which might contribute to the suppression of plasma lipid levels by activated IRE1α. Ablation of XBP1 ameliorated hepatosteatosis, liver damage, and hypercholesterolemia in dyslipidemic animal models, suggesting that direct targeting of either IRE1α or XBP1 might be a feasible strategy to treat dyslipidemias.
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Affiliation(s)
- Jae-Seon So
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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27
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Moon YA, Liang G, Xie X, Frank-Kamenetsky M, Fitzgerald K, Koteliansky V, Brown MS, Goldstein JL, Horton JD. The Scap/SREBP pathway is essential for developing diabetic fatty liver and carbohydrate-induced hypertriglyceridemia in animals. Cell Metab 2012; 15:240-6. [PMID: 22326225 PMCID: PMC3662050 DOI: 10.1016/j.cmet.2011.12.017] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 11/28/2011] [Accepted: 12/24/2011] [Indexed: 12/19/2022]
Abstract
Insulin resistance leads to hypertriglyceridemia and hepatic steatosis and is associated with increased SREBP-1c, a transcription factor that activates fatty acid synthesis. Here, we show that steatosis in insulin-resistant ob/ob mice was abolished by deletion of Scap, an escort protein necessary for generating nuclear isoforms of all three SREBPs. Scap deletion reduced lipid synthesis and prevented fatty livers despite persistent obesity, hyperinsulinemia, and hyperglycemia. Scap deficiency also prevented steatosis in mice fed high-fat diets. Steatosis was also prevented when siRNAs were used to silence Scap in livers of sucrose-fed hamsters, a model of diet-induced steatosis and hypertriglyceridemia. This silencing reduced all three nuclear SREBPs, decreasing lipid biosynthesis and abolishing sucrose-induced hypertriglyceridemia. These results demonstrate that SREBP activation is essential for development of diabetic hepatic steatosis and carbohydrate-induced hypertriglyceridemia, but not insulin resistance. Inhibition of SREBP activation has therapeutic potential for treatment of hypertriglyceridemia and fatty liver disease.
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Affiliation(s)
- Young-Ah Moon
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
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28
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Hur KY, So JS, Ruda V, Frank-Kamenetsky M, Fitzgerald K, Koteliansky V, Iwawaki T, Glimcher LH, Lee AH. IRE1α activation protects mice against acetaminophen-induced hepatotoxicity. ACTA ACUST UNITED AC 2012; 209:307-18. [PMID: 22291093 PMCID: PMC3280871 DOI: 10.1084/jem.20111298] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The mammalian stress sensor IRE1α plays a central role in the unfolded protein, or endoplasmic reticulum (ER), stress response by activating its downstream transcription factor XBP1 via an unconventional splicing mechanism. IRE1α can also induce the degradation of a subset of mRNAs in a process termed regulated IRE1-dependent decay (RIDD). Although diverse mRNA species can be degraded by IRE1α in vitro, the pathophysiological functions of RIDD are only beginning to be explored. Acetaminophen (APAP) overdose is the most frequent cause of acute liver failure in young adults in the United States and is primarily caused by CYP1A2-, CYP2E1-, and CYP3A4-driven conversion of APAP into hepatotoxic metabolites. We demonstrate here that genetic ablation of XBP1 results in constitutive IRE1α activation in the liver, leading to RIDD of Cyp1a2 and Cyp2e1 mRNAs, reduced JNK activation, and protection of mice from APAP-induced hepatotoxicity. A pharmacological ER stress inducer that activated IRE1α suppressed the expression of Cyp1a2 and Cyp2e1 in WT, but not IRE1α-deficient mouse liver, indicating the essential role of IRE1α in the down-regulation of these mRNAs upon ER stress. Our study reveals an unexpected function of RIDD in drug metabolism.
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Affiliation(s)
- Kyu Yeon Hur
- Deartment of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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29
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Novobrantseva TI, Borodovsky A, Wong J, Klebanov B, Zafari M, Yucius K, Querbes W, Ge P, Ruda VM, Milstein S, Speciner L, Duncan R, Barros S, Basha G, Cullis P, Akinc A, Donahoe JS, Narayanannair Jayaprakash K, Jayaraman M, Bogorad RL, Love K, Whitehead K, Levins C, Manoharan M, Swirski FK, Weissleder R, Langer R, Anderson DG, de Fougerolles A, Nahrendorf M, Koteliansky V. Systemic RNAi-mediated Gene Silencing in Nonhuman Primate and Rodent Myeloid Cells. Mol Ther Nucleic Acids 2012; 1:e4. [PMID: 23344621 PMCID: PMC3381593 DOI: 10.1038/mtna.2011.3] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Leukocytes are central regulators of inflammation and the target cells of therapies for key diseases, including autoimmune, cardiovascular, and malignant disorders. Efficient in vivo delivery of small interfering RNA (siRNA) to immune cells could thus enable novel treatment strategies with broad applicability. In this report, we develop systemic delivery methods of siRNA encapsulated in lipid nanoparticles (LNP) for durable and potent in vivo RNA interference (RNAi)-mediated silencing in myeloid cells. This work provides the first demonstration of siRNA-mediated silencing in myeloid cell types of nonhuman primates (NHPs) and establishes the feasibility of targeting multiple gene targets in rodent myeloid cells. The therapeutic potential of these formulations was demonstrated using siRNA targeting tumor necrosis factor-α (TNFα) which induced substantial attenuation of disease progression comparable to a potent antibody treatment in a mouse model of rheumatoid arthritis (RA). In summary, we demonstrate a broadly applicable and therapeutically relevant platform for silencing disease genes in immune cells.
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30
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Leuschner F, Dutta P, Gorbatov R, Novobrantseva TI, Donahoe JS, Courties G, Lee KM, Kim JI, Markmann JF, Marinelli B, Panizzi P, Lee WW, Iwamoto Y, Milstein S, Epstein-Barash H, Cantley W, Wong J, Cortez-Retamozo V, Newton A, Love K, Libby P, Pittet MJ, Swirski FK, Koteliansky V, Langer R, Weissleder R, Anderson DG, Nahrendorf M. Therapeutic siRNA silencing in inflammatory monocytes in mice. Nat Biotechnol 2011; 29:1005-10. [PMID: 21983520 PMCID: PMC3212614 DOI: 10.1038/nbt.1989] [Citation(s) in RCA: 625] [Impact Index Per Article: 48.1] [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: 07/13/2011] [Accepted: 08/29/2011] [Indexed: 12/24/2022]
Abstract
Inflammatory monocytes -- but not the non-inflammatory subset -- depend on the chemokine receptor CCR2 for distribution to injured tissue and stimulate disease progression. Precise therapeutic targeting of this inflammatory monocyte subset could spare innate immunity's essential functions for maintenance of homeostasis and thus limit unwanted effects. Here we developed siRNA nanoparticles targeting CCR2 expression in inflammatory monocytes. We identified an optimized lipid nanoparticle and silencing siRNA sequence that when administered systemically, had rapid blood clearance, accumulated in spleen and bone marrow and showed high cellular localization of fluorescently tagged siRNA inside monocytes. Efficient degradation of CCR2 mRNA in monocytes prevented their accumulation in sites of inflammation. Specifically, the treatment attenuated their number in atherosclerotic plaques, reduced infarct size following coronary artery occlusion, prolonged normoglycemia in diabetic mice after pancreatic islet transplantation and resulted in reduced tumor volumes and lower numbers of tumor-associated macrophages. Taken together, siRNA nanoparticle-mediated CCR2 gene silencing in leukocytes selectively modulates functions of innate immune cell subtypes and may allow for the development of specific anti-inflammatory therapy.
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Affiliation(s)
- Florian Leuschner
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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31
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Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, Li X, Li H, Kuperwasser N, Ruda VM, Pirruccello JP, Muchmore B, Prokunina-Olsson L, Hall JL, Schadt EE, Morales CR, Lund-Katz S, Phillips MC, Wong J, Cantley W, Racie T, Ejebe KG, Orho-Melander M, Melander O, Koteliansky V, Fitzgerald K, Krauss RM, Cowan CA, Kathiresan S, Rader DJ. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 2010; 466:714-9. [PMID: 20686566 DOI: 10.1038/nature09266] [Citation(s) in RCA: 825] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 06/09/2010] [Indexed: 12/27/2022]
Abstract
Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 strongly associated with both plasma low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. Here we show through a series of studies in human cohorts and human-derived hepatocytes that a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP (CCAAT/enhancer binding protein) transcription factor binding site and alters the hepatic expression of the SORT1 gene. With small interfering RNA (siRNA) knockdown and viral overexpression in mouse liver, we demonstrate that Sort1 alters plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we provide functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We also demonstrate that common noncoding DNA variants identified by GWASs can directly contribute to clinical phenotypes.
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Affiliation(s)
- Kiran Musunuru
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
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32
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Akinc A, Querbes W, De S, Qin J, Frank-Kamenetsky M, Jayaprakash KN, Jayaraman M, Rajeev KG, Cantley WL, Dorkin JR, Butler JS, Qin L, Racie T, Sprague A, Fava E, Zeigerer A, Hope MJ, Zerial M, Sah DWY, Fitzgerald K, Tracy MA, Manoharan M, Koteliansky V, Fougerolles AD, Maier MA. Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol Ther 2010; 18:1357-64. [PMID: 20461061 DOI: 10.1038/mt.2010.85] [Citation(s) in RCA: 742] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lipid nanoparticles (LNPs) have proven to be highly efficient carriers of short-interfering RNAs (siRNAs) to hepatocytes in vivo; however, the precise mechanism by which this efficient delivery occurs has yet to be elucidated. We found that apolipoprotein E (apoE), which plays a major role in the clearance and hepatocellular uptake of physiological lipoproteins, also acts as an endogenous targeting ligand for ionizable LNPs (iLNPs), but not cationic LNPs (cLNPs). The role of apoE was investigated using both in vitro studies employing recombinant apoE and in vivo studies in wild-type and apoE(-/-) mice. Receptor dependence was explored in vitro and in vivo using low-density lipoprotein receptor (LDLR(-/-))-deficient mice. As an alternative to endogenous apoE-based targeting, we developed a targeting approach using an exogenous ligand containing a multivalent N-acetylgalactosamine (GalNAc)-cluster, which binds with high affinity to the asialoglycoprotein receptor (ASGPR) expressed on hepatocytes. Both apoE-based endogenous and GalNAc-based exogenous targeting appear to be highly effective strategies for the delivery of iLNPs to liver.
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Affiliation(s)
- Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA.
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33
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Akinc A, Goldberg M, Qin J, Dorkin JR, Gamba-Vitalo C, Maier M, Jayaprakash KN, Jayaraman M, Rajeev KG, Manoharan M, Koteliansky V, Röhl I, Leshchiner ES, Langer R, Anderson DG. Development of lipidoid-siRNA formulations for systemic delivery to the liver. Mol Ther 2009; 17:872-9. [PMID: 19259063 DOI: 10.1038/mt.2009.36] [Citation(s) in RCA: 255] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA interference therapeutics afford the potential to silence target gene expression specifically, thereby blocking production of disease-causing proteins. The development of safe and effective systemic small interfering RNA (siRNA) delivery systems is of central importance to the therapeutic application of siRNA. Lipid and lipid-like materials are currently the most well-studied siRNA delivery systems for liver delivery, having been utilized in several animal models, including nonhuman primates. Here, we describe the development of a multicomponent, systemic siRNA delivery system, based on the novel lipid-like material 98N(12)-5(1). We show that in vivo delivery efficacy is affected by many parameters, including the formulation composition, nature of particle PEGylation, degree of drug loading, and biophysical parameters such as particle size. In particular, small changes in the anchor chain length of poly(ethylene glycol) (PEG) lipids can result in significant effects on in vivo efficacy. The lead formulation developed is liver targeted (>90% injected dose distributes to liver) and can induce fully reversible, long-duration gene silencing without loss of activity following repeat administration.
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Affiliation(s)
- Akin Akinc
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts 02142, USA.
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34
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Thum T, Gross C, Fiedler J, Fischer T, Kissler S, Bussen M, Galuppo P, Just S, Rottbauer W, Frantz S, Castoldi M, Soutschek J, Koteliansky V, Rosenwald A, Basson MA, Licht JD, Pena JTR, Rouhanifard SH, Muckenthaler MU, Tuschl T, Martin GR, Bauersachs J, Engelhardt S. MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature 2008; 456:980-4. [PMID: 19043405 DOI: 10.1038/nature07511] [Citation(s) in RCA: 1825] [Impact Index Per Article: 114.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Accepted: 10/03/2008] [Indexed: 01/06/2023]
Abstract
MicroRNAs comprise a broad class of small non-coding RNAs that control expression of complementary target messenger RNAs. Dysregulation of microRNAs by several mechanisms has been described in various disease states including cardiac disease. Whereas previous studies of cardiac disease have focused on microRNAs that are primarily expressed in cardiomyocytes, the role of microRNAs expressed in other cell types of the heart is unclear. Here we show that microRNA-21 (miR-21, also known as Mirn21) regulates the ERK-MAP kinase signalling pathway in cardiac fibroblasts, which has impacts on global cardiac structure and function. miR-21 levels are increased selectively in fibroblasts of the failing heart, augmenting ERK-MAP kinase activity through inhibition of sprouty homologue 1 (Spry1). This mechanism regulates fibroblast survival and growth factor secretion, apparently controlling the extent of interstitial fibrosis and cardiac hypertrophy. In vivo silencing of miR-21 by a specific antagomir in a mouse pressure-overload-induced disease model reduces cardiac ERK-MAP kinase activity, inhibits interstitial fibrosis and attenuates cardiac dysfunction. These findings reveal that microRNAs can contribute to myocardial disease by an effect in cardiac fibroblasts. Our results validate miR-21 as a disease target in heart failure and establish the therapeutic efficacy of microRNA therapeutic intervention in a cardiovascular disease setting.
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Affiliation(s)
- Thomas Thum
- Department of Medicine I, Interdisziplinäres Zentrum für Klinische Forschung (IZKF), University of Wuerzburg, 97080 Wuerzburg, Germany
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35
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Rodrigues CD, Hannus M, Prudêncio M, Martin C, Gonçalves LA, Portugal S, Epiphanio S, Akinc A, Hadwiger P, Jahn-Hofmann K, Röhl I, van Gemert GJ, Franetich JF, Luty AJF, Sauerwein R, Mazier D, Koteliansky V, Vornlocher HP, Echeverri CJ, Mota MM. Host scavenger receptor SR-BI plays a dual role in the establishment of malaria parasite liver infection. Cell Host Microbe 2008; 4:271-82. [PMID: 18779053 DOI: 10.1016/j.chom.2008.07.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 06/27/2008] [Accepted: 07/18/2008] [Indexed: 12/29/2022]
Abstract
An obligatory step of malaria parasite infection is Plasmodium sporozoite invasion of host hepatocytes, and host lipoprotein clearance pathways have been linked to Plasmodium liver infection. By using RNA interference to screen lipoprotein-related host factors, we show here that the class B, type I scavenger receptor (SR-BI) is the strongest regulator of Plasmodium infection among these factors. Inhibition of SR-BI function reduced P. berghei infection in Huh7 cells, and overexpression of SR-BI led to increased infection. In vivo silencing of liver SR-BI expression in mice and inhibition of SR-BI activity in human primary hepatocytes reduced infection by P. berghei and by P. falciparum, respectively. Heterozygous SR-BI(+/-) mice displayed reduced P. berghei infection rates correlating with liver SR-BI expression levels. Additional analyses revealed that SR-BI plays a dual role in Plasmodium infection, affecting both sporozoite invasion and intracellular parasite development, and may therefore constitute a good target for malaria prophylaxis.
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Affiliation(s)
- Cristina D Rodrigues
- Unidade de Malária, Instituto de Medicina Molecular, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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36
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John M, Constien R, Akinc A, Goldberg M, Moon YA, Spranger M, Hadwiger P, Soutschek J, Vornlocher HP, Manoharan M, Stoffel M, Langer R, Anderson DG, Horton JD, Koteliansky V, Bumcrot D. Effective RNAi-mediated gene silencing without interruption of the endogenous microRNA pathway. Nature 2007; 449:745-7. [PMID: 17898712 PMCID: PMC3019095 DOI: 10.1038/nature06179] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 08/16/2007] [Indexed: 12/03/2022]
Abstract
Systemic administration of synthetic small interfering RNAs (siRNAs) effectively silences hepatocyte gene expression in rodents and primates. Whether or not in vivo gene silencing by synthetic siRNA can disrupt the endogenous microRNA (miRNA) pathway remains to be addressed. Here we show that effective target-gene silencing in the mouse and hamster liver can be achieved by systemic administration of synthetic siRNA without any demonstrable effect on miRNA levels or activity. Indeed, siRNA targeting two hepatocyte-specific genes (apolipoprotein B and factor VII) that achieved efficient (approximately 80%) silencing of messenger RNA transcripts and a third irrelevant siRNA control were administered to mice without significant changes in the levels of three hepatocyte-expressed miRNAs (miR-122, miR-16 and let-7a) or an effect on miRNA activity. Moreover, multiple administrations of an siRNA targeting the hepatocyte-expressed gene Scap in hamsters achieved long-term mRNA silencing without significant changes in miR-122 levels. This study advances the use of siRNAs as safe and effective tools to silence gene transcripts in animal studies, and supports the continued advancement of RNA interference therapeutics using synthetic siRNA.
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Affiliation(s)
- Matthias John
- Alnylam Europe AG, Fritz-Hornschuch-Str. 9, 95326 Kulmbach, Germany
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37
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Wolfrum C, Shi S, Jayaprakash KN, Jayaraman M, Wang G, Pandey RK, Rajeev KG, Nakayama T, Charrise K, Ndungo EM, Zimmermann T, Koteliansky V, Manoharan M, Stoffel M. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nat Biotechnol 2007; 25:1149-57. [PMID: 17873866 DOI: 10.1038/nbt1339] [Citation(s) in RCA: 709] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Accepted: 08/27/2007] [Indexed: 12/11/2022]
Abstract
Cholesterol-conjugated siRNAs can silence gene expression in vivo. Here we synthesize a variety of lipophilic siRNAs and use them to elucidate the requirements for siRNA delivery in vivo. We show that conjugation to bile acids and long-chain fatty acids, in addition to cholesterol, mediates siRNA uptake into cells and gene silencing in vivo. Efficient and selective uptake of these siRNA conjugates depends on interactions with lipoprotein particles, lipoprotein receptors and transmembrane proteins. High-density lipoprotein (HDL) directs siRNA delivery into liver, gut, kidney and steroidogenic organs, whereas low-density lipoprotein (LDL) targets siRNA primarily to the liver. LDL-receptor expression is essential for siRNA delivery by LDL particles, and SR-BI receptor expression is required for uptake of HDL-bound siRNAs. Cellular uptake also requires the mammalian homolog of the Caenorhabditis elegans transmembrane protein Sid1. Our results demonstrate that conjugation to lipophilic molecules enables effective siRNA uptake through a common mechanism that can be exploited to optimize therapeutic siRNA delivery.
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Affiliation(s)
- Christian Wolfrum
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Zürich, HPT E73
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38
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Abstract
The rapid identification of highly specific and potent drug candidates continues to be a substantial challenge with traditional pharmaceutical approaches. Moreover, many targets have proven to be intractable to traditional small-molecule and protein approaches. Therapeutics based on RNA interference (RNAi) offer a powerful method for rapidly identifying specific and potent inhibitors of disease targets from all molecular classes. Numerous proof-of-concept studies in animal models of human disease demonstrate the broad potential application of RNAi therapeutics. The major challenge for successful drug development is identifying delivery strategies that can be translated to the clinic. With advances in this area and the commencement of multiple clinical trials with RNAi therapeutic candidates, a transformation in modern medicine may soon be realized.
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Affiliation(s)
- David Bumcrot
- Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, 02142 Massachusetts USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, 02142 Massachusetts USA
| | - Victor Koteliansky
- Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, 02142 Massachusetts USA
| | - Dinah W Y Sah
- Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, 02142 Massachusetts USA
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39
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Zimmermann TS, Lee ACH, Akinc A, Bramlage B, Bumcrot D, Fedoruk MN, Harborth J, Heyes JA, Jeffs LB, John M, Judge AD, Lam K, McClintock K, Nechev LV, Palmer LR, Racie T, Röhl I, Seiffert S, Shanmugam S, Sood V, Soutschek J, Toudjarska I, Wheat AJ, Yaworski E, Zedalis W, Koteliansky V, Manoharan M, Vornlocher HP, MacLachlan I. RNAi-mediated gene silencing in non-human primates. Nature 2006; 441:111-4. [PMID: 16565705 DOI: 10.1038/nature04688] [Citation(s) in RCA: 994] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 03/06/2006] [Indexed: 02/07/2023]
Abstract
The opportunity to harness the RNA interference (RNAi) pathway to silence disease-causing genes holds great promise for the development of therapeutics directed against targets that are otherwise not addressable with current medicines. Although there are numerous examples of in vivo silencing of target genes after local delivery of small interfering RNAs (siRNAs), there remain only a few reports of RNAi-mediated silencing in response to systemic delivery of siRNA, and there are no reports of systemic efficacy in non-rodent species. Here we show that siRNAs, when delivered systemically in a liposomal formulation, can silence the disease target apolipoprotein B (ApoB) in non-human primates. APOB-specific siRNAs were encapsulated in stable nucleic acid lipid particles (SNALP) and administered by intravenous injection to cynomolgus monkeys at doses of 1 or 2.5 mg kg(-1). A single siRNA injection resulted in dose-dependent silencing of APOB messenger RNA expression in the liver 48 h after administration, with maximal silencing of >90%. This silencing effect occurred as a result of APOB mRNA cleavage at precisely the site predicted for the RNAi mechanism. Significant reductions in ApoB protein, serum cholesterol and low-density lipoprotein levels were observed as early as 24 h after treatment and lasted for 11 days at the highest siRNA dose, thus demonstrating an immediate, potent and lasting biological effect of siRNA treatment. Our findings show clinically relevant RNAi-mediated gene silencing in non-human primates, supporting RNAi therapeutics as a potential new class of drugs.
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Affiliation(s)
- Tracy S Zimmermann
- Alnylam Pharmaceuticals Inc., 300 Third Street, Cambridge, Massachusetts 02142, USA.
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40
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Novobrantseva TI, Majeau GR, Amatucci A, Kogan S, Brenner I, Casola S, Shlomchik MJ, Koteliansky V, Hochman PS, Ibraghimov A. Attenuated liver fibrosis in the absence of B cells. J Clin Invest 2006; 115:3072-82. [PMID: 16276416 PMCID: PMC1265860 DOI: 10.1172/jci24798] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 08/23/2005] [Indexed: 12/15/2022] Open
Abstract
Analysis of mononuclear cells in the adult mouse liver revealed that B cells represent as much as half of the intrahepatic lymphocyte population. Intrahepatic B cells (IHB cells) are phenotypically similar to splenic B2 cells but express lower levels of CD23 and CD21 and higher levels of CD5. IHB cells proliferate as well as splenic B cells in response to anti-IgM and LPS stimulation in vitro. VDJ gene rearrangements in IHB cells contain insertions of N,P region nucleotides characteristic of B cells maturing in the adult bone marrow rather than in the fetal liver. To evaluate whether B cells can have an impact on liver pathology, we compared CCl4-induced fibrosis development in B cell-deficient and wild-type mice. CCl4 caused similar acute liver injury in mutant and wild-type mice. However, following 6 weeks of CCl4 treatment, histochemical analyses showed markedly reduced collagen deposition in B cell-deficient as compared with wild-type mice. By analyzing mice that have normal numbers of B cells but lack either T cells or immunoglobulin in the serum, we established that B cells have an impact on fibrosis in an antibody- and T cell-independent manner.
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41
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Schapira K, Lutgens E, de Fougerolles A, Sprague A, Roemen A, Gardner H, Koteliansky V, Daemen M, Heeneman S. Genetic Deletion or Antibody Blockade of α1β1 Integrin Induces a Stable Plaque Phenotype in ApoE−/− Mice. Arterioscler Thromb Vasc Biol 2005; 25:1917-24. [PMID: 15976328 DOI: 10.1161/01.atv.0000174807.90292.2f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [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: 11/16/2022]
Abstract
Objective—
Adhesive interactions between cells and the extracellular matrix play an important role in inflammatory diseases like atherosclerosis. We investigated the role of the collagen-binding integrin α1β1 in atherosclerosis.
Methods and Results—
ApoE−/− mice were α1-deficient or received early or delayed anti-α1 antibody treatment. Deficiency in α1 integrin reduced the area of atherosclerotic plaques and altered plaque composition by reducing inflammation and increasing extracellular matrix. In advanced plaques, α1-deficient mice had a reduced macrophage and CD3+ cell content, collagen and smooth muscle cell content increased, lipid core sizes decreased, and cartilaginous metaplasia occurred. Anti-α1 antibody treatment reduced the macrophage content in initial plaques after early and delayed treatment, decreased the CD3+ cell content in advanced plaques after delayed treatment, and increased the collagen content in initial and advanced plaques after delayed treatment. Migration assays performed on α1-deficient macrophages on collagen I and IV substrata revealed that α1-deficient cells can migrate on collagen I, but not IV. Anti-α1 antibody treatment of ApoE−/− macrophages also inhibited migration of cells on collagen IV.
Conclusions—
Our results suggest that α1β1 integrin is involved in atherosclerosis by mediating the migration of leukocytes to lesions by adhesion to collagen IV. Blocking this integrin reduces atherosclerosis and induces a stable plaque phenotype.
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Affiliation(s)
- Kitty Schapira
- Department of Pathology, Cardiovascular Research Institute Maastricht, University of Maastricht, Maastricht, The Netherlands
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42
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Lutgens E, Faber B, Schapira K, Evelo CTA, van Haaften R, Heeneman S, Cleutjens KBJM, Bijnens AP, Beckers L, Porter JG, Mackay CR, Rennert P, Bailly V, Jarpe M, Dolinski B, Koteliansky V, de Fougerolles T, Daemen MJAP. Gene Profiling in Atherosclerosis Reveals a Key Role for Small Inducible Cytokines. Circulation 2005; 111:3443-52. [PMID: 15967845 DOI: 10.1161/circulationaha.104.510073] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Pathological aspects of atherosclerosis are well described, but gene profiles during atherosclerotic plaque progression are largely unidentified.
Methods and Results—
Microarray analysis was performed on mRNA of aortic arches of ApoE
−/−
mice fed normal chow (NC group) or Western-type diet (WD group) for 3, 4.5, and 6 months. Of 10 176 reporters, 387 were differentially (>2×) expressed in at least 1 group compared with a common reference (ApoE
−/−
, 3- month NC group). The number of differentially expressed genes increased during plaque progression. Time-related expression clustering and functional grouping of differentially expressed genes suggested important functions for genes involved in inflammation (especially the small inducible cytokines monocyte chemoattractant protein [MCP]-1, MCP-5, macrophage inflammatory protein [MIP]-1α, MIP-1β, MIP-2, and fractalkine) and matrix degradation (cathepsin-S, matrix metalloproteinase-2/12). Validation experiments focused on the gene cluster of small inducible cytokines. Real-time polymerase chain reaction revealed a plaque progression–dependent increase in mRNA levels of MCP-1, MCP-5, MIP-1α, and MIP-1β. ELISA for MCP-1 and MCP-5 showed similar results. Immunohistochemistry for MCP-1, MCP-5, and MIP-1α located their expression to plaque macrophages. An inhibiting antibody for MCP-1 and MCP-5 (11K2) was designed and administered to ApoE
−/−
mice for 12 weeks starting at the age of 5 or 17 weeks. 11K2 treatment reduced plaque area and macrophage and CD45
+
cell content and increased collagen content, thereby inducing a stable plaque phenotype.
Conclusions—
Gene profiling of atherosclerotic plaque progression in ApoE
−/−
mice revealed upregulation of the gene cluster of small inducible cytokines. Further expression and in vivo validation studies showed that this gene cluster mediates plaque progression and stability.
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Affiliation(s)
- Esther Lutgens
- Department of Pathology, Cardiovascular Research Institute Maastricht, University of Maastricht, Maastricht, The Netherlands.
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43
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Soutschek J, Akinc A, Bramlage B, Charisse K, Constien R, Donoghue M, Elbashir S, Geick A, Hadwiger P, Harborth J, John M, Kesavan V, Lavine G, Pandey RK, Racie T, Rajeev KG, Röhl I, Toudjarska I, Wang G, Wuschko S, Bumcrot D, Koteliansky V, Limmer S, Manoharan M, Vornlocher HP. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 2004; 432:173-8. [PMID: 15538359 DOI: 10.1038/nature03121] [Citation(s) in RCA: 1620] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Accepted: 10/20/2004] [Indexed: 01/10/2023]
Abstract
RNA interference (RNAi) holds considerable promise as a therapeutic approach to silence disease-causing genes, particularly those that encode so-called 'non-druggable' targets that are not amenable to conventional therapeutics such as small molecules, proteins, or monoclonal antibodies. The main obstacle to achieving in vivo gene silencing by RNAi technologies is delivery. Here we show that chemically modified short interfering RNAs (siRNAs) can silence an endogenous gene encoding apolipoprotein B (apoB) after intravenous injection in mice. Administration of chemically modified siRNAs resulted in silencing of the apoB messenger RNA in liver and jejunum, decreased plasma levels of apoB protein, and reduced total cholesterol. We also show that these siRNAs can silence human apoB in a transgenic mouse model. In our in vivo study, the mechanism of action for the siRNAs was proven to occur through RNAi-mediated mRNA degradation, and we determined that cleavage of the apoB mRNA occurred specifically at the predicted site. These findings demonstrate the therapeutic potential of siRNAs for the treatment of disease.
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MESH Headings
- Animals
- Apolipoprotein B-100
- Apolipoproteins B/blood
- Apolipoproteins B/deficiency
- Apolipoproteins B/genetics
- Cholesterol/blood
- Disease Models, Animal
- Genetic Therapy/methods
- Humans
- Injections, Intravenous
- Jejunum/drug effects
- Jejunum/metabolism
- Liver/drug effects
- Liver/metabolism
- Mice
- Mice, Transgenic
- RNA Interference/drug effects
- RNA Processing, Post-Transcriptional/drug effects
- RNA Stability
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- Sensitivity and Specificity
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Affiliation(s)
- Jürgen Soutschek
- Alnylam Europe AG, Fritz-Hornschuch-Str. 9, 95326 Kulmbach, Germany.
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44
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Ray SJ, Franki SN, Pierce RH, Dimitrova S, Koteliansky V, Sprague AG, Doherty PC, de Fougerolles AR, Topham DJ. The collagen binding alpha1beta1 integrin VLA-1 regulates CD8 T cell-mediated immune protection against heterologous influenza infection. Immunity 2004; 20:167-79. [PMID: 14975239 DOI: 10.1016/s1074-7613(04)00021-4] [Citation(s) in RCA: 250] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Accepted: 01/01/2004] [Indexed: 11/22/2022]
Abstract
A common feature of many infections is that many pathogen-specific memory T cells become established in diverse nonlymphoid tissues. A mechanism that promotes the retention and survival of the memory T cells in diverse tissues has not been described. Our studies show that the collagen binding alpha1beta1 integrin, VLA-1, is expressed by the majority of influenza-specific CD8 T cells recovered from nonlymphoid tissues during both the acute and memory phases of the response. Antibody treatment or genetic deficiency of VLA-1 decreased virus-specific CTL in the lung and other nonlymphoid tissues, and increased them in the spleen. In spite of the increase in the spleen, secondary heterosubtypic immunity against flu was compromised. This suggests that VLA-1 is responsible for retaining protective memory CD8 T cells in the lung and other tissues via attachment to the extracellular matrix.
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Affiliation(s)
- Steven J Ray
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester, Rochester, NY 14642, USA
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45
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Gardner H, Strehlow D, Bradley L, Widom R, Farina A, de Fougerolles A, Peyman J, Koteliansky V, Korn JH. Global expression analysis of the fibroblast transcriptional response to TGFbeta. Clin Exp Rheumatol 2004; 22:S47-57. [PMID: 15344598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
OBJECTIVES Transforming Growth Factor-beta (TGFbeta) is the predominant cytokine in all forms of fibrotic reactions. As well as being secreted by immune modulators of fibrosis such as macrophages, it is involved in an autocrine feedback loop of fibroblast stimulation whose regulation is still poorly understood. We wished to gain some insight into the mechanisms of the fibroblast response to TGFbeta. METHODS We undertook an exhaustive transcript profiling experiment using a widely validated restriction enzyme based method for identifying differentially expressed genes (GeneCalling). Transcriptional responses throughout a 24-hour time course were examined at multiple time points and classified. RESULTS By 24 hours of TGF treatment over 1000 bands, representing a large number of transcripts, were down- or upregulated greater than 2-fold. All of the known genes responsive to TGFbeta, such as collagen and connective tissue growth factor, were upregulated. CONCLUSIONS This encyclopedic method revealed many unknown transcriptional responses to TGFbeta including the upregulation of a variety of less expected cytoskeletal and matrix components, as well as interactions between the TGFbeta and tumor necrosis factor (TNF) pathways and alterations in cell death-related pathways. These may in part explain the idiosyncratic responses of mesenchymal cells to TGFbeta.
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Affiliation(s)
- H Gardner
- Biogen Inc, Cambridge, Massachusetts, USA
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46
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Rodgers KD, Rao V, Meehan DT, Fager N, Gotwals P, Ryan ST, Koteliansky V, Nemori R, Cosgrove D. Monocytes may promote myofibroblast accumulation and apoptosis in Alport renal fibrosis. Kidney Int 2003; 63:1338-55. [PMID: 12631350 DOI: 10.1046/j.1523-1755.2003.00871.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [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] [Indexed: 01/20/2023]
Abstract
BACKGROUND In interstitial fibrosis, monocytes and myofibroblasts have been directly implicated in scarring, apoptosis, and tissue necrosis. While much has been done to explore the role of these cell types individually in fibrosis, the interactive dependency of monocytes and myofibroblasts has been only marginally explored. METHODS Alport mice were treated or not with a soluble receptor inhibitor for transforming growth factor-beta 1 (TGF-beta 1), which was previously shown to inhibit the accumulation of myofibroblasts, but not monocytes, in the tubulointerstitium. Kidneys were examined for fibrosis using several matrix markers, TGF-beta 1 mRNA expression by in situ hybridization, apoptosis using the terminal deoxynucleotidyl transferase-mediated uridine triphosphate nick end labeling (TUNEL) assay, expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPS) by dual immunofluorescence microscopy, MMP activity by gelatin and in situ zymography, MMP mRNA expression by reverse transcription-polymerase chain reaction (RT-PCR), and basement membrane degradation by dual immunofluorescence confocal microscopy and electron microscopy. RESULTS Treated mice showed a markedly reduced accumulation of matrix proteins. Tissue monocytes express TGF-beta 1 mRNA, and TGF-beta 1 is required for myofibroblast accumulation. The number of apoptotic cells was not influenced by TGF-beta 1 inhibition. Monocytes express MMP-2, MMP-9, TIMP-2, and TIMP-3. MMP activity and mRNA expression is equally up regulated in treated and untreated Alport mice. Tubular basement membranes (TBM) around clusters of monocytes are notably degraded. TGF-beta 1 inhibition does not extend the life of Alport mice. CONCLUSION These studies demonstrate that monocytes may influence myofibroblast accumulation via TGF-beta1, and that monocytes, and not myofibroblasts, are associated with tubular atrophy in Alport mice. Elevated MMP expression and activity is associated with TBM destruction near monocytes clusters, suggesting an anoikis mechanism may contribute to apoptosis in this model.
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Affiliation(s)
- Kathyrn D Rodgers
- Department of Genetics, Boys Town National Research Hospital, Omaha, Nebraska 68131, USA
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47
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Klein S, de Fougerolles AR, Blaikie P, Khan L, Pepe A, Green CD, Koteliansky V, Giancotti FG. Alpha 5 beta 1 integrin activates an NF-kappa B-dependent program of gene expression important for angiogenesis and inflammation. Mol Cell Biol 2002; 22:5912-22. [PMID: 12138201 PMCID: PMC133962 DOI: 10.1128/mcb.22.16.5912-5922.2002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [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: 01/13/2023] Open
Abstract
GeneCalling, a genome-wide method of mRNA profiling, reveals that endothelial cells adhering to fibronectin through the alpha 5 beta 1 integrin, but not to laminin through the alpha 2 beta 1 integrin, undergo a complex program of gene expression. Several of the genes identified are regulated by the NF-kappa B transcription factor, and many are implicated in the regulation of inflammation and angiogenesis. Adhesion of endothelial cells to fibronectin activates NF-kappa B through a signaling pathway requiring Ras, phosphatidylinositol 3-kinase, and Rho family proteins, whereas adhesion to laminin has a limited effect. Retroviral transfer of the superrepressor of NF-kappa B, I kappa B-2A, blocks basic fibroblast growth factor-induced angiogenesis in vivo. These results suggest that engagement of the alpha 5 beta 1 integrin promotes an NF-kappa B-dependent program of gene expression that coordinately regulates angiogenesis and inflammation.
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Affiliation(s)
- Sharon Klein
- Cellular Biochemistry and Biophysics Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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48
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Muraoka RS, Dumont N, Ritter CA, Dugger TC, Brantley DM, Chen J, Easterly E, Roebuck LR, Ryan S, Gotwals PJ, Koteliansky V, Arteaga CL. Blockade of TGF-beta inhibits mammary tumor cell viability, migration, and metastases. J Clin Invest 2002; 109:1551-9. [PMID: 12070302 PMCID: PMC151012 DOI: 10.1172/jci15234] [Citation(s) in RCA: 204] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
TGF-betas are potent inhibitors of epithelial cell proliferation. However, in established carcinomas, autocrine/paracrine TGF-beta interactions can enhance tumor cell viability and progression. Thus, we studied the effect of a soluble Fc:TGF-beta type II receptor fusion protein (Fc:TbetaRII) on transgenic and transplantable models of breast cancer metastases. Systemic administration of Fc:TbetaRII did not alter primary mammary tumor latency in MMTV-Polyomavirus middle T antigen transgenic mice. However, Fc:TbetaRII increased apoptosis in primary tumors, while reducing tumor cell motility, intravasation, and lung metastases. These effects correlated with inhibition of Akt activity and FKHRL1 phosphorylation. Fc:TbetaRII also inhibited metastases from transplanted 4T1 and EMT-6 mammary tumors in syngeneic BALB/c mice. Tumor microvessel density in a mouse dorsal skin window chamber was unaffected by Fc:TbetaRII. Therefore, blockade of TGF-beta signaling may reduce tumor cell viability and migratory potential and represents a testable therapeutic approach against metastatic carcinomas.
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MESH Headings
- Animals
- Antigens, Polyomavirus Transforming/genetics
- Apoptosis
- Autocrine Communication
- Breast/drug effects
- Breast/pathology
- Cell Movement
- Cell Survival
- Female
- Genetic Vectors
- Immunoglobulin Fc Fragments/administration & dosage
- Immunoglobulin Fc Fragments/genetics
- Immunoglobulin Fc Fragments/physiology
- Immunoglobulin G/administration & dosage
- Immunoglobulin G/genetics
- Immunoglobulin G/physiology
- Lung Neoplasms/secondary
- Mammary Neoplasms, Animal/pathology
- Mammary Tumor Virus, Mouse
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Neoplasm Metastasis
- Neovascularization, Pathologic
- Protein Serine-Threonine Kinases
- Receptor, Transforming Growth Factor-beta Type II
- Receptors, Transforming Growth Factor beta/administration & dosage
- Receptors, Transforming Growth Factor beta/immunology
- Receptors, Transforming Growth Factor beta/physiology
- Recombinant Fusion Proteins/administration & dosage
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/pharmacology
- Signal Transduction
- Solubility
- Transforming Growth Factor beta/antagonists & inhibitors
- Transforming Growth Factor beta/metabolism
- Transforming Growth Factor beta/pharmacology
- Transforming Growth Factor beta1
- Tumor Cells, Cultured
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Affiliation(s)
- Rebecca S Muraoka
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 27232, USA
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49
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Muraoka RS, Dumont N, Ritter CA, Dugger TC, Brantley DM, Chen J, Easterly E, Roebuck LR, Ryan S, Gotwals PJ, Koteliansky V, Arteaga CL. Blockade of TGF-β inhibits mammary tumor cell viability, migration, and metastases. J Clin Invest 2002. [DOI: 10.1172/jci0215234] [Citation(s) in RCA: 384] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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50
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Yata Y, Gotwals P, Koteliansky V, Rockey DC. Dose-dependent inhibition of hepatic fibrosis in mice by a TGF-beta soluble receptor: implications for antifibrotic therapy. Hepatology 2002; 35:1022-30. [PMID: 11981752 DOI: 10.1053/jhep.2002.32673] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Transforming growth factor (TGF) beta isoforms (in particular, TGF-beta1) play a central role in the fibrogenic response to injury in many organs, including the liver. Although TGF-beta is clearly important in fibrogenesis, a number of issues related to therapeutic antagonism have emerged. For example, the long-term effect of TGF-beta antagonism is unknown; furthermore, controversy exists as to appropriate levels of TGF-beta inhibition. Therefore, we aimed to examine TGF-beta in models of chronic liver injury and to determine whether an in vivo dose-response relationship exists for inhibition of TGF-beta. Liver injury was induced in BALB/c mice by administering carbon tetrachloride for 4 or 8 weeks. TGF-beta binding was inhibited with a soluble TGF-beta type II receptor (STR) construct, administered intraperitoneally over a dose range of 4.0, 1.0, 0.4, or 0.1 mg/kg twice weekly during fibrogenesis. Fibrogenesis was assessed by measurement of type I collagen messenger RNA (mRNA) expression and by quantitative morphometric analysis. In the 4-week study, STR at concentrations of 4.0, 1.0, and 0.1 mg/kg reduced type I collagen mRNA expression by 31%, 49%, and 60% compared with immunoglobulin (Ig) G controls, respectively. In the 8-week study, lower concentrations of STR (0.1 mg/kg) also had the greatest effect on type I collagen mRNA expression. Quantitative morphometrics similarly showed that lower concentrations of STR were the most antifibrogenic. In conclusion, the results confirm the antifibrotic effect of inhibiting TGF-beta in chronic hepatic wounding and, moreover, show that its in vivo effect in the mouse is dose dependent. Such findings have major translational implications for therapeutic strategies aimed at TGF-beta.
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Affiliation(s)
- Yutaka Yata
- Liver Center and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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