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Molina Vargas A, Sinha S, Osborn R, Arantes P, Patel A, Dewhurst S, Hardy D, Cameron A, Palermo G, O’Connell M. New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity. Nucleic Acids Res 2024; 52:921-939. [PMID: 38033324 PMCID: PMC10810210 DOI: 10.1093/nar/gkad1132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that can be deployed at point-of-care. Recently, the RNA-guided ribonuclease CRISPR-Cas13 has been successfully harnessed for such purposes. However, developing assays for detection of genetic variability, for example single-nucleotide polymorphisms, is still challenging and previously described design strategies are not always generalizable. Here, we expanded our characterization of LbuCas13a RNA-detection specificity by performing a combination of experimental RNA mismatch tolerance profiling, molecular dynamics simulations, protein, and crRNA engineering. We found certain positions in the crRNA-target-RNA duplex that are particularly sensitive to mismatches and establish the effect of RNA concentration in mismatch tolerance. Additionally, we determined that shortening the crRNA spacer or modifying the direct repeat of the crRNA leads to stricter specificities. Furthermore, we harnessed our understanding of LbuCas13a allosteric activation pathways through molecular dynamics and structure-guided engineering to develop novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. We deployed these Cas13a variants and crRNA design strategies to achieve superior discrimination of SARS-CoV-2 strains compared to wild-type LbuCas13a. Together, our work provides new design criteria and Cas13a variants to use in future easier-to-implement Cas13-based RNA detection applications.
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Affiliation(s)
- Adrian M Molina Vargas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Souvik Sinha
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Raven Osborn
- Clinical and Translational Sciences Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Amun Patel
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Stephen Dewhurst
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Dwight J Hardy
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Mitchell R O’Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
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2
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Nie X, Wang D, Pan Y, Hua Y, Lü P, Yang Y. Discovery, classification and application of the CPISPR-Cas13 system. Technol Health Care 2024; 32:525-544. [PMID: 37545273 DOI: 10.3233/thc-230258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins. OBJECTIVE This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance. METHODS Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed. RESULTS The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA. CONCLUSION The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.
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Affiliation(s)
- Xiaojuan Nie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Pan
- School of Experimental Animal Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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3
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Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557474. [PMID: 37745416 PMCID: PMC10515814 DOI: 10.1101/2023.09.12.557474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.
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Affiliation(s)
- Megan D Schertzer
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Andrew Stirn
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Keren Isaev
- New York Genome Center, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
| | | | - Anjali Das
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | | | - Stella H Park
- New York Genome Center, New York, NY
- Department of Biomedical Engineering, Columbia University, New York, NY
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - Neville E Sanjana
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - David A Knowles
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
- Data Science Institute, Columbia University, New York, NY
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4
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Vargas AMM, Osborn R, Sinha S, Arantes PR, Patel A, Dewhurst S, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550755. [PMID: 37547020 PMCID: PMC10402140 DOI: 10.1101/2023.07.26.550755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that can be deployed at point-of-care. Recently, the RNA-guided ribonuclease CRISPR-Cas13 has been successfully harnessed for such purposes. However, developing assays for detection of genetic variability, for example single-nucleotide polymorphisms, is still challenging and previously described design strategies are not always generalizable. Here, we expanded our characterization of LbuCas13a RNA-detection specificity by performing a combination of experimental RNA mismatch tolerance profiling, molecular dynamics simulations, protein, and crRNA engineering. We found certain positions in the crRNA-target-RNA duplex that are particularly sensitive to mismatches and establish the effect of RNA concentration in mismatch tolerance. Additionally, we determined that shortening the crRNA spacer or modifying the direct repeat of the crRNA leads to stricter specificities. Furthermore, we harnessed our understanding of LbuCas13a allosteric activation pathways through molecular dynamics and structure-guided engineering to develop novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. We deployed these Cas13a variants and crRNA design strategies to achieve superior discrimination of SARS-CoV-2 strains compared to wild-type LbuCas13a. Together, our work provides new design criteria and new Cas13a variants for easier-to-implement Cas13-based diagnostics. KEY POINTS Certain positions in the Cas13a crRNA-target-RNA duplex are particularly sensitive to mismatches.Understanding Cas13a's allosteric activation pathway allowed us to develop novel high-fidelity Cas13a variants.These Cas13a variants and crRNA design strategies achieve superior discrimination of SARS-CoV-2 strains. GRAPHICAL ABSTRACT
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5
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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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6
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Knott GJ, Lapinaite A, O'Connell MR. Methods special issue: RNA-targeting technologies. Methods 2023; 212:10-11. [PMID: 36792042 DOI: 10.1016/j.ymeth.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Affiliation(s)
- Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC, Australia
| | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA; Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA; Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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7
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Wessels HH, Méndez-Mancilla A, Hao Y, Papalexi E, Mauck WM, Lu L, Morris JA, Mimitou EP, Smibert P, Sanjana NE, Satija R. Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nat Methods 2023; 20:86-94. [PMID: 36550277 PMCID: PMC10030154 DOI: 10.1038/s41592-022-01705-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Here, we introduce Cas13 RNA Perturb-seq (CaRPool-seq), which leverages the RNA-targeting CRISPR-Cas13d system and enables efficient combinatorial perturbations alongside multimodal single-cell profiling. CaRPool-seq encodes multiple perturbations on a cleavable CRISPR array that is associated with a detectable barcode sequence, allowing for the simultaneous targeting of multiple genes. We compared CaRPool-seq to existing Cas9-based methods, highlighting its unique strength to efficiently profile combinatorially perturbed cells. Finally, we apply CaRPool-seq to perform multiplexed combinatorial perturbations of myeloid differentiation regulators in an acute myeloid leukemia (AML) model system and identify extensive interactions between different chromatin regulators that can enhance or suppress AML differentiation phenotypes.
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Affiliation(s)
- Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Yuhan Hao
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Efthymia Papalexi
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - William M Mauck
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Lu Lu
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - John A Morris
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eleni P Mimitou
- New York Genome Center, New York, NY, USA
- Technology Innovation Laboratory, New York Genome Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA
- Technology Innovation Laboratory, New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA.
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
| | - Rahul Satija
- New York Genome Center, New York, NY, USA.
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
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