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Nakamura H, Lee AA, Afshar AS, Watanabe S, Rho E, Razavi S, Suarez A, Lin YC, Tanigawa M, Huang B, DeRose R, Bobb D, Hong W, Gabelli SB, Goutsias J, Inoue T. Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions. Nat Mater 2018; 17:79-89. [PMID: 29115293 PMCID: PMC5916848 DOI: 10.1038/nmat5006] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 09/08/2017] [Indexed: 05/06/2023]
Abstract
Some protein components of intracellular non-membrane-bound entities, such as RNA granules, are known to form hydrogels in vitro. The physico-chemical properties and functional role of these intracellular hydrogels are difficult to study, primarily due to technical challenges in probing these materials in situ. Here, we present iPOLYMER, a strategy for a rapid induction of protein-based hydrogels inside living cells that explores the chemically inducible dimerization paradigm. Biochemical and biophysical characterizations aided by computational modelling show that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that acts as a size-dependent molecular sieve. We functionalize these polymers with RNA-binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. These results show that iPOLYMER can be used to synthetically reconstitute the nucleation of biologically functional entities, including RNA granules in intact cells.
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Affiliation(s)
- Hideki Nakamura
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Albert A. Lee
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Ali Sobhi Afshar
- Center for Imaging Science, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD, 21218
- To whom correspondence regarding the computational analysis should be addressed: (A.S.A)
| | - Shigeki Watanabe
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
| | - Elmer Rho
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Shiva Razavi
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218
| | - Allison Suarez
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Yu-Chun Lin
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Makoto Tanigawa
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218
| | - Brian Huang
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Robert DeRose
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - Diana Bobb
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
| | - William Hong
- Department of Biophysics and Biophysical Chemistry, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205
| | - John Goutsias
- Center for Imaging Science, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD, 21218
| | - Takanari Inoue
- Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 21205
- Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218
- To whom general correspondence should be addressed: (T.I.)
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Afshar AS, Xu J, Goutsias J. Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer. PLoS One 2014; 9:e100806. [PMID: 24968068 PMCID: PMC4072696 DOI: 10.1371/journal.pone.0100806] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 01/20/2014] [Accepted: 05/28/2014] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) have attracted a great deal of attention in biology and medicine. It has been hypothesized that miRNAs interact with transcription factors (TFs) in a coordinated fashion to play key roles in regulating signaling and transcriptional pathways and in achieving robust gene regulation. Here, we propose a novel integrative computational method to infer certain types of deregulated miRNA-mediated regulatory circuits at the transcriptional, post-transcriptional and signaling levels. To reliably predict miRNA-target interactions from mRNA/miRNA expression data, our method collectively utilizes sequence-based miRNA-target predictions obtained from several algorithms, known information about mRNA and miRNA targets of TFs available in existing databases, certain molecular structures identified to be statistically over-represented in gene regulatory networks, available molecular subtyping information, and state-of-the-art statistical techniques to appropriately constrain the underlying analysis. In this way, the method exploits almost every aspect of extractable information in the expression data. We apply our procedure on mRNA/miRNA expression data from prostate tumor and normal samples and detect numerous known and novel miRNA-mediated deregulated loops and networks in prostate cancer. We also demonstrate instances of the results in a number of distinct biological settings, which are known to play crucial roles in prostate and other types of cancer. Our findings show that the proposed computational method can be used to effectively achieve notable insights into the poorly understood molecular mechanisms of miRNA-mediated interactions and dissect their functional roles in cancer in an effort to pave the way for miRNA-based therapeutics in clinical settings.
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Affiliation(s)
- Ali Sobhi Afshar
- Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Joseph Xu
- Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
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