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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
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Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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Abstract
CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems.
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Affiliation(s)
- Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Assael A Madrigal
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kevin D Dong
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Smargon AA, Shi YJ, Yeo GW. RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering. Nat Cell Biol 2020; 22:143-150. [PMID: 32015437 PMCID: PMC8008746 DOI: 10.1038/s41556-019-0454-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 03/21/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, we chart progress in the RNA-targeting CRISPR-Cas (RCas) field and illustrate how continuing evolution in scientific discovery translates into applications for RNA biology and insights into mysteries, obstacles, and alternative technologies that lie ahead.
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Affiliation(s)
- Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yilan J Shi
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.
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Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F. Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. Mol Cell 2017; 65:618-630.e7. [PMID: 28065598 PMCID: PMC5432119 DOI: 10.1016/j.molcel.2016.12.023] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [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: 11/10/2016] [Revised: 12/06/2016] [Accepted: 12/23/2016] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity. Using an E. coli essential gene screen, we demonstrate that Cas13b has a double-sided protospacer-flanking sequence and elucidate RNA secondary structure requirements for targeting. We also find that Csx27 represses, whereas Csx28 enhances, Cas13b-mediated RNA interference. Characterization of these CRISPR systems creates opportunities to develop tools to manipulate and monitor cellular transcripts.
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Affiliation(s)
- Aaron A Smargon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B T Cox
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neena K Pyzocha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kaijie Zheng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian M Slaymaker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Omar A Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Essletzbichler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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