1
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Yao Y, Zhou Z, Wang X, Liu Z, Zhai Y, Chi X, Du J, Luo L, Zhao Z, Wang X, Xue C, Rao S. SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. CELL GENOMICS 2024:100583. [PMID: 38889719 DOI: 10.1016/j.xgen.2024.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/28/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024]
Abstract
CRISPR mutagenesis screens conducted with SpCas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (PAM) sequences. Here, leveraging the broad targeting scope of the near-PAMless SpRY variant, we have demonstrated that saturated SpRY mutagenesis and base editing screens can faithfully identify functional regulatory elements and essential genetic variants for target gene expression at single-base resolution. We further extended this methodology to investigate a genome-wide association study (GWAS) locus at 10q22.1 associated with a red blood cell trait, where we identified potential enhancers regulating HK1 gene expression, despite not all of these enhancers exhibiting typical chromatin signatures. More importantly, our saturated base editing screens pinpoint multiple causal variants within this locus that would otherwise be missed by Bayesian statistical fine-mapping. Our approach is generally applicable to functional interrogation of all non-coding genomic elements while complementing other high-coverage CRISPR screens.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Xiaoling Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Zhirui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yixin Zhai
- Department of Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaolin Chi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingyi Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Liheng Luo
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zhigang Zhao
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Xiaoyue Wang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
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2
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Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP, Li X, Pang B. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs. Nat Biomed Eng 2024:10.1038/s41551-024-01204-8. [PMID: 38778183 DOI: 10.1038/s41551-024-01204-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
The functions of non-coding regulatory elements (NCREs), which constitute a major fraction of the human genome, have not been systematically studied. Here we report a method involving libraries of paired single-guide RNAs targeting both ends of an NCRE as a screening system for the Cas9-mediated deletion of thousands of NCREs genome-wide to study their functions in distinct biological contexts. By using K562 and 293T cell lines and human embryonic stem cells, we show that NCREs can have redundant functions, and that many ultra-conserved elements have silencer activity and play essential roles in cell growth and in cellular responses to drugs (notably, the ultra-conserved element PAX6_Tarzan may be critical for heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation). The high-throughput screen, which is compatible with single-cell sequencing, may allow for the identification of druggable NCREs.
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Affiliation(s)
- Yufeng Li
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Minkang Tan
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Almira Akkari-Henić
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Limin Zhang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten Kip
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Shengnan Sun
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jorian J Sepers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ningning Xu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Susan L Kloet
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Harald Mikkers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua J Gruber
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Xiao Li
- Department of Biochemistry, The Center for RNA Science and Therapeutics, Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Baoxu Pang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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3
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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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4
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Wessels HH, Stirn A, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA, Sanjana NE. Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning. Nat Biotechnol 2024; 42:628-637. [PMID: 37400521 DOI: 10.1038/s41587-023-01830-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/16/2023] [Indexed: 07/05/2023]
Abstract
Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes in human cells with systematically designed mismatches and insertions and deletions (indels). We find that mismatches and indels have a position- and context-dependent impact on Cas13d activity, and mismatches that result in G-U wobble pairings are better tolerated than other single-base mismatches. Using this large-scale dataset, we train a convolutional neural network that we term targeted inhibition of gene expression via gRNA design (TIGER) to predict efficacy from guide sequence and context. TIGER outperforms the existing models at predicting on-target and off-target activity on our dataset and published datasets. We show that TIGER scoring combined with specific mismatches yields the first general framework to modulate transcript expression, enabling the use of RNA-targeting CRISPRs to precisely control gene dosage.
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Affiliation(s)
- Hans-Hermann Wessels
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Andrew Stirn
- New York Genome Center, New York City, NY, USA
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Eric J Kim
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Sydney K Hart
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - David A Knowles
- New York Genome Center, New York City, NY, USA.
- Department of Computer Science, Columbia University, New York City, NY, USA.
- Data Science Institute, Columbia University, New York City, NY, USA.
- Department of Systems Biology, Columbia University, New York City, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York City, NY, USA.
- Department of Biology, New York University, New York City, NY, USA.
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5
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Walton RT, Qin Y, Blainey PC. CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585235. [PMID: 38558968 PMCID: PMC10979941 DOI: 10.1101/2024.03.17.585235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are incompatible with pooled screening methodologies that require mRNA-embedded barcodes, including some microscopy and single cell sequencing approaches. Here, we report the development of CROPseq-multi, a CROPseq1-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with mRNA-embedded barcodes. CROPseq-multi has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. CROPseq-multi is compatible with enrichment screening methodologies and optical pooled screens, and is extensible to screens with single-cell sequencing readouts. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode detection efficiency 10-fold, enables detection of recombination events, and increases decoding efficiency 3-fold relative to CROPseq. CROPseq-multi is a widely applicable multiplexing solution for diverse SpCas9-based genetic screening approaches.
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Affiliation(s)
- Russell T. Walton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Yue Qin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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6
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Clark T, Waller MA, Loo L, Moreno CL, Denes CE, Neely GG. CRISPR activation screens: navigating technologies and applications. Trends Biotechnol 2024:S0167-7799(24)00036-2. [PMID: 38493051 DOI: 10.1016/j.tibtech.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) has become an integral part of the molecular biology toolkit. CRISPRa genetic screens are an exciting high-throughput means of identifying genes the upregulation of which is sufficient to elicit a given phenotype. Activation machinery is continually under development to achieve greater, more robust, and more consistent activation. In this review, we offer a succinct technological overview of available CRISPRa architectures and a comprehensive summary of pooled CRISPRa screens. Furthermore, we discuss contemporary applications of CRISPRa across broad fields of research, with the aim of presenting a view of exciting emerging applications for CRISPRa screening.
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Affiliation(s)
- Teleri Clark
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Christopher E Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia.
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7
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McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Escude Velasco B, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. CELL GENOMICS 2024; 4:100519. [PMID: 38484704 PMCID: PMC10943585 DOI: 10.1016/j.xgen.2024.100519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/31/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
The diversity of CRISPR systems, coupled with scientific ingenuity, has led to an explosion of applications; however, to test newly described innovations in their model systems, researchers typically embark on cumbersome, one-off cloning projects to generate custom reagents that are optimized for their biological questions. Here, we leverage Golden Gate cloning to create the Fragmid toolkit, a modular set of CRISPR cassettes and delivery technologies, along with a web portal, resulting in a combinatorial platform that enables scalable vector assembly within days. We further demonstrate that multiple CRISPR technologies can be assessed in parallel in a pooled screening format using this resource, enabling the rapid optimization of both novel technologies and cellular models. These results establish Fragmid as a robust system for the rapid design of CRISPR vectors, and we anticipate that this assembly approach will be broadly useful for systematic development, comparison, and dissemination of CRISPR technologies.
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Affiliation(s)
- Abby V McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yanjing V Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Audrey L Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zsofia M Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronte Wen
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carolyn Kraus
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nathan W Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Berta Escude Velasco
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan D Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew A Greene
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas M Green
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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8
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Kim N, Choi S, Kim S, Song M, Seo JH, Min S, Park J, Cho SR, Kim HH. Deep learning models to predict the editing efficiencies and outcomes of diverse base editors. Nat Biotechnol 2024; 42:484-497. [PMID: 37188916 DOI: 10.1038/s41587-023-01792-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
Applications of base editing are frequently restricted by the requirement for a protospacer adjacent motif (PAM), and selecting the optimal base editor (BE) and single-guide RNA pair (sgRNA) for a given target can be difficult. To select for BEs and sgRNAs without extensive experimental work, we systematically compared the editing windows, outcomes and preferred motifs for seven BEs, including two cytosine BEs, two adenine BEs and three C•G to G•C BEs at thousands of target sequences. We also evaluated nine Cas9 variants that recognize different PAM sequences and developed a deep learning model, DeepCas9variants, for predicting which variants function most efficiently at sites with a given target sequence. We then develop a computational model, DeepBE, that predicts editing efficiencies and outcomes of 63 BEs that were generated by incorporating nine Cas9 variants as nickase domains into the seven BE variants. The predicted median efficiencies of BEs with DeepBE-based design were 2.9- to 20-fold higher than those of rationally designed SpCas9-containing BEs.
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Affiliation(s)
- Nahye Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungchul Choi
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungjae Kim
- Precision Medicine Institute, Macrogen, Seoul, Republic of Korea
| | - Myungjae Song
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwa Seo
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung-Rae Cho
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea
- Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Otolaryngology, University of California, San Francisco, CA, USA.
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9
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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10
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Rios X, Pardias O, Morales MA, Bhattacharya P, Chen Y, Guo L, Zhang C, Di Pierro EJ, Tian G, Barragan GA, Sumazin P, Metelitsa LS. Refining chimeric antigen receptors via barcoded protein domain combination pooled screening. Mol Ther 2023; 31:3210-3224. [PMID: 37705245 PMCID: PMC10638030 DOI: 10.1016/j.ymthe.2023.09.008] [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] [Received: 02/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
Chimeric antigen receptor (CAR)-T cells represent a promising frontier in cancer immunotherapy. However, the current process for developing new CAR constructs is time consuming and inefficient. To address this challenge and expedite the evaluation and comparison of full-length CAR designs, we have devised a novel cloning strategy. This strategy involves the sequential assembly of individual CAR domains using blunt ligation, with each domain being assigned a unique DNA barcode. Applying this method, we successfully generated 360 CAR constructs that specifically target clinically validated tumor antigens CD19 and GD2. By quantifying changes in barcode frequencies through next-generation sequencing, we characterize CARs that best mediate proliferation and expansion of transduced T cells. The screening revealed a crucial role for the hinge domain in CAR functionality, with CD8a and IgG4 hinges having opposite effects in the surface expression, cytokine production, and antitumor activity in CD19- versus GD2-based CARs. Importantly, we discovered two novel CD19-CAR architectures containing the IgG4 hinge domain that mediate superior in vivo antitumor activity compared with the construct used in Kymriah, a U.S. Food and Drug Administration (FDA)-approved therapy. This novel screening approach represents a major advance in CAR engineering, enabling accelerated development of cell-based cancer immunotherapies.
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Affiliation(s)
- Xavier Rios
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Osmay Pardias
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Marc A Morales
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Pradyot Bhattacharya
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yibin Chen
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Linjie Guo
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chunchao Zhang
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Erica J Di Pierro
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gengwen Tian
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Gabriel A Barragan
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Pavel Sumazin
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Leonid S Metelitsa
- Center for Advanced Innate Cell Therapy, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.
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11
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McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Velasco BE, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564061. [PMID: 37961518 PMCID: PMC10634825 DOI: 10.1101/2023.10.25.564061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The diversity of CRISPR systems, coupled with scientific ingenuity, has led to an explosion of applications; however, to test newly-described innovations in their model systems, researchers typically embark on cumbersome, one-off cloning projects to generate custom reagents that are optimized for their biological questions. Here, we leverage Golden Gate cloning to create the Fragmid toolkit, a modular set of CRISPR cassettes and delivery technologies, along with a web portal, resulting in a combinatorial platform that enables scalable vector assembly within days. We further demonstrate that multiple CRISPR technologies can be assessed in parallel in a pooled screening format using this resource, enabling the rapid optimization of both novel technologies and cellular models. These results establish Fragmid as a robust system for the rapid design of CRISPR vectors, and we anticipate that this assembly approach will be broadly useful for systematic development, comparison, and dissemination of CRISPR technologies.
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Affiliation(s)
- Abby V McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yanjing V Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Audrey L Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zsofia M Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronte Wen
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carolyn Kraus
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nathan W Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Berta Escude Velasco
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan D Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew A Greene
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas M Green
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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12
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Blaeschke F, Chen YY, Apathy R, Daniel B, Chen AY, Chen PA, Sandor K, Zhang W, Li Z, Mowery CT, Yamamoto TN, Nyberg WA, To A, Yu R, Bueno R, Kim MC, Schmidt R, Goodman DB, Feuchtinger T, Eyquem J, Jimmie Ye C, Carnevale J, Satpathy AT, Shifrut E, Roth TL, Marson A. Modular pooled discovery of synthetic knockin sequences to program durable cell therapies. Cell 2023; 186:4216-4234.e33. [PMID: 37714135 PMCID: PMC10508323 DOI: 10.1016/j.cell.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 04/22/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.
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Affiliation(s)
- Franziska Blaeschke
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan Apathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Andy Y Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Peixin Amy Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Wenxi Zhang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cody T Mowery
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tori N Yamamoto
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - William A Nyberg
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Angela To
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ruby Yu
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Raymund Bueno
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Min Cheol Kim
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel B Goodman
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA
| | - Tobias Feuchtinger
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich 80337, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Munich 80336, Germany; National Center for Infection Research (DZIF), Munich 81377, Germany
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Carnevale
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Eric Shifrut
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Theodore L Roth
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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13
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Griffith AL, Zheng F, McGee AV, Miller NW, Szegletes ZM, Reint G, Gademann F, Nwolah I, Hegde M, Liu YV, Goodale A, Doench JG. Optimization of Cas12a for multiplexed genome-scale transcriptional activation. CELL GENOMICS 2023; 3:100387. [PMID: 37719144 PMCID: PMC10504673 DOI: 10.1016/j.xgen.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 09/19/2023]
Abstract
Cas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here, we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results with those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
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Affiliation(s)
- Audrey L. Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fengyi Zheng
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Abby V. McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Nathan W. Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Zsofia M. Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ganna Reint
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fabian Gademann
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ifunanya Nwolah
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Yanjing V. Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
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14
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Seo SY, Min S, Lee S, Seo JH, Park J, Kim HK, Song M, Baek D, Cho SR, Kim HH. Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s. Nat Methods 2023:10.1038/s41592-023-01875-2. [PMID: 37188955 DOI: 10.1038/s41592-023-01875-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Recently, various small Cas9 orthologs and variants have been reported for use in in vivo delivery applications. Although small Cas9s are particularly suited for this purpose, selecting the most optimal small Cas9 for use at a specific target sequence continues to be challenging. Here, to this end, we have systematically compared the activities of 17 small Cas9s for thousands of target sequences. For each small Cas9, we have characterized the protospacer adjacent motif and determined optimal single guide RNA expression formats and scaffold sequence. High-throughput comparative analyses revealed distinct high- and low-activity groups of small Cas9s. We also developed DeepSmallCas9, a set of computational models predicting the activities of the small Cas9s at matched and mismatched target sequences. Together, this analysis and these computational models provide a useful guide for researchers to select the most suitable small Cas9 for specific applications.
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Affiliation(s)
- Sang-Yeon Seo
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Sungtae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwa Seo
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Myungjae Song
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dawoon Baek
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Rehabilitation Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Sung-Rae Cho
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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15
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Skinner OS, Blanco-Fernández J, Goodman RP, Kawakami A, Shen H, Kemény LV, Joesch-Cohen L, Rees MG, Roth JA, Fisher DE, Mootha VK, Jourdain AA. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nat Metab 2023; 5:765-776. [PMID: 37198474 PMCID: PMC10229423 DOI: 10.1038/s42255-023-00774-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 05/19/2023]
Abstract
Glucose is vital for life, serving as both a source of energy and carbon building block for growth. When glucose is limiting, alternative nutrients must be harnessed. To identify mechanisms by which cells can tolerate complete loss of glucose, we performed nutrient-sensitized genome-wide genetic screens and a PRISM growth assay across 482 cancer cell lines. We report that catabolism of uridine from the medium enables the growth of cells in the complete absence of glucose. While previous studies have shown that uridine can be salvaged to support pyrimidine synthesis in the setting of mitochondrial oxidative phosphorylation deficiency1, our work demonstrates that the ribose moiety of uridine or RNA can be salvaged to fulfil energy requirements via a pathway based on: (1) the phosphorylytic cleavage of uridine by uridine phosphorylase UPP1/UPP2 into uracil and ribose-1-phosphate (R1P), (2) the conversion of uridine-derived R1P into fructose-6-P and glyceraldehyde-3-P by the non-oxidative branch of the pentose phosphate pathway and (3) their glycolytic utilization to fuel ATP production, biosynthesis and gluconeogenesis. Capacity for glycolysis from uridine-derived ribose appears widespread, and we confirm its activity in cancer lineages, primary macrophages and mice in vivo. An interesting property of this pathway is that R1P enters downstream of the initial, highly regulated steps of glucose transport and upper glycolysis. We anticipate that 'uridine bypass' of upper glycolysis could be important in the context of disease and even exploited for therapeutic purposes.
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Affiliation(s)
- Owen S Skinner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Russell P Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Hongying Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
- Yale Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Dermatology, Venereology and Dermatooncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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16
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Zheng Y, VanDusen NJ. Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements. J Cardiovasc Dev Dis 2023; 10:jcdd10040144. [PMID: 37103023 PMCID: PMC10146671 DOI: 10.3390/jcdd10040144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic cis-regulatory elements, generation of mice featuring transgenic reporters or cis-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research.
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17
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Kim YH, Kim N, Okafor I, Choi S, Min S, Lee J, Bae SM, Choi K, Choi J, Harihar V, Kim Y, Kim JS, Kleinstiver BP, Lee JK, Ha T, Kim HH. Sniper2L is a high-fidelity Cas9 variant with high activity. Nat Chem Biol 2023:10.1038/s41589-023-01279-5. [PMID: 36894722 PMCID: PMC10374439 DOI: 10.1038/s41589-023-01279-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023]
Abstract
Although several high-fidelity SpCas9 variants have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper-Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences and developed DeepSniper, a deep learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.
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Affiliation(s)
- Young-Hoon Kim
- Toolgen, Seoul, Republic of Korea.,Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea
| | - Nahye Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ikenna Okafor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sungchul Choi
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | | | | | | | - Janice Choi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Vinayak Harihar
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jin-Soo Kim
- Department of Biochemistry and NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea. .,Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Center for Nanomedicine, Institute for Basic Science, Seoul, Republic of Korea. .,Yonsei-Institute for Basic Science Institute, Yonsei University, Seoul, Republic of Korea. .,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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18
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Cheng J, Lin G, Wang T, Wang Y, Guo W, Liao J, Yang P, Chen J, Shao X, Lu X, Zhu L, Wang Y, Fan X. Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204484. [PMID: 36504444 PMCID: PMC9896079 DOI: 10.1002/advs.202204484] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single-cell CRISPR screening (scCRISPR) techniques, which result from the combination of single-cell toolkits and CRISPR screening, allow dissecting regulatory networks in complex biological systems at unprecedented resolution. These methods allow cells to be perturbed en masse using a pooled CRISPR library, followed by high-content phenotyping. This is technically accomplished by annotating cells with sgRNA-specific barcodes or directly detectable sgRNAs. According to the integration of distinct single-cell technologies, these methods principally fall into four categories: scCRISPR with RNA-seq, scCRISPR with ATAC-seq, scCRISPR with proteome probing, and imaging-based scCRISPR. scCRISPR has deciphered genotype-phenotype relationships, genetic regulations, tumor biological issues, and neuropathological mechanisms. This review provides insight into the technical breakthrough of scCRISPR by systematically summarizing the advancements of various scCRISPR methodologies and analyzing their merits and limitations. In addition, an application-oriented approach guide is offered to meet researchers' individualized demands.
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Affiliation(s)
- Junyun Cheng
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Gaole Lin
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Tianhao Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Yunzhu Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Wenbo Guo
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Liao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Penghui Yang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jie Chen
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xin Shao
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiaoyan Lu
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
| | - Ling Zhu
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
| | - Yi Wang
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
| | - Xiaohui Fan
- Pharmaceutical Informatics InstituteCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
- State Key Laboratory of Component‐Based Chinese MedicineInnovation Center in Zhejiang UniversityHangzhou310058China
- Jinhua Institute of Zhejiang UniversityJinhua321016China
- The Save Sight InstituteFaculty of Medicine and Healththe University of SydneySydneyNSW2000Australia
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxing314100China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
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19
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Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
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Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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20
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A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens. Cell Syst 2022; 13:376-387.e8. [PMID: 35316656 DOI: 10.1016/j.cels.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/27/2021] [Accepted: 02/25/2022] [Indexed: 12/16/2022]
Abstract
Pooled genetic libraries have improved screening throughput for mapping genotypes to phenotypes. However, selectable phenotypes are limited, restricting screening to outcomes with a low spatiotemporal resolution. Here, we integrated live-cell imaging with pooled library-based screening. To enable intracellular multiplexing, we developed a method called EPICode that uses a combination of short epitopes, which can also appear in various subcellular locations. EPICode thus enables the use of live-cell microscopy to characterize a phenotype of interest over time, including after sequential stimulatory/inhibitory manipulations, and directly connects behavior to the cellular genotype. To test EPICode's capacity against an important milestone-engineering and optimizing dynamic, live-cell reporters-we developed a live-cell PKA kinase translocation reporter with improved sensitivity and specificity. The use of epitopes as fluorescent barcodes introduces a scalable strategy for high-throughput screening broadly applicable to protein engineering and drug discovery settings where image-based phenotyping is desired.
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21
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Li S, Qian N, Jiang C, Zu W, Liang A, Li M, Elledge SJ, Tan X. Gain-of-function genetic screening identifies the antiviral function of TMEM120A via STING activation. Nat Commun 2022; 13:105. [PMID: 35013224 PMCID: PMC8748537 DOI: 10.1038/s41467-021-27670-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/01/2021] [Indexed: 02/08/2023] Open
Abstract
Zika virus (ZIKV) infection can be associated with neurological pathologies, such as microcephaly in newborns and Guillain-Barre syndrome in adults. Effective therapeutics are currently not available. As such, a comprehensive understanding of virus-host interactions may guide the development of medications for ZIKV. Here we report a human genome-wide overexpression screen to identify host factors that regulate ZIKV infection and find TMEM120A as a ZIKV restriction factor. TMEM120A overexpression significantly inhibits ZIKV replication, while TMEM120A knockdown increases ZIKV infection in cell lines. Moreover, Tmem120a knockout in mice facilitates ZIKV infection in primary mouse embryonic fibroblasts (MEF) cells. Mechanistically, the antiviral activity of TMEM120A is dependent on STING, as TMEM120A interacts with STING, promotes the translocation of STING from the endoplasmic reticulum (ER) to ER-Golgi intermediate compartment (ERGIC) and enhances the phosphorylation of downstream TBK1 and IRF3, resulting in the expression of multiple antiviral cytokines and interferon-stimulated genes. In summary, our gain-of-function screening identifies TMEM120A as a key activator of the antiviral signaling of STING. Understanding the interplay between host and viral factors during infection is essential for the interactome of infection. Here the authors perform a gain-of-function screen to identify factors involved during Zika virus infection and identify TMEM120A as a key factor in the STING mediated immune responses.
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Affiliation(s)
- Shuo Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Nianchao Qian
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Chao Jiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Wenhong Zu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Anthony Liang
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02120, USA
| | - Mamie Li
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02120, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02120, USA
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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22
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Parekh U, McDonald D, Dailamy A, Wu Y, Cordes T, Zhang K, Tipps A, Metallo C, Mali P. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas. iScience 2021; 24:103149. [PMID: 34646987 PMCID: PMC8496177 DOI: 10.1016/j.isci.2021.103149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 11/22/2022] Open
Abstract
Deconstructing tissue-specific effects of genes and variants on proliferation is critical to understanding cellular transformation and systematically selecting cancer therapeutics. This requires scalable methods for multiplexed genetic screens tracking fitness across time, across lineages, and in a suitable niche, since physiological cues influence functional differences. Towards this, we present an approach, coupling single-cell cancer driver screens in teratomas with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serial reinjection. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. Additionally, mutant MEK1 S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful platform for multi-lineage longitudinal study of oncogenesis.
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Affiliation(s)
- Udit Parekh
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, USA
| | - Daniella McDonald
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, USA
| | - Amir Dailamy
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Yan Wu
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Thekla Cordes
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Ann Tipps
- School of Medicine, University of California San Diego, San Diego, USA
| | - Christian Metallo
- Department of Bioengineering, University of California San Diego, San Diego, USA
- Salk Institute of Biological Studies, La Jolla, USA
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, San Diego, USA
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23
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Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening. Nat Protoc 2021; 16:4722-4765. [PMID: 34508260 DOI: 10.1038/s41596-021-00595-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/17/2021] [Indexed: 02/08/2023]
Abstract
CRISPR-based forward genetic screening represents a powerful approach for the systematic characterization of gene function. Recent efforts have been directed toward establishing CRISPR-based tools for the programmable delivery of combinatorial genetic perturbations, most of which are mediated by a single nuclease and the expression of structurally identical guide backbones from two promoters. In contrast, we have developed CHyMErA (Cas hybrid for multiplexed editing and screening applications), which is based on the co-expression of Cas9 and Cas12a nucleases in conjunction with a hybrid guide RNA (hgRNA) engineered by the fusion of Cas9 and Cas12a guides and expressed from a single U6 promoter. CHyMErA is suitable for the high-throughput deletion of genetic segments including the excision of individual exons. Furthermore, CHyMErA enables the concomitant targeting of two or more genes and can thus be used for the systematic mapping of genetic interactions in mammalian cells. CHyMErA can also be applied for the perturbation of paralogous gene pairs, thereby allowing the capturing of phenotypic roles that would otherwise be masked because of genetic redundancy. Here, we provide instructions for the cloning of hgRNA screening libraries and individual hgRNA constructs and offer guidelines for designing and performing combinatorial pooled genetic screens using CHyMErA. Starting with the generation of Cas9- and Cas12a-expressing cell lines, CHyMErA screening can be implemented within 15-20 weeks.
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24
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Kim HK, Yu G, Park J, Min S, Lee S, Yoon S, Kim HH. Predicting the efficiency of prime editing guide RNAs in human cells. Nat Biotechnol 2021; 39:198-206. [PMID: 32958957 DOI: 10.1038/s41587-020-0677-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
Abstract
Prime editing enables the introduction of virtually any small-sized genetic change without requiring donor DNA or double-strand breaks. However, evaluation of prime editing efficiency requires time-consuming experiments, and the factors that affect efficiency have not been extensively investigated. In this study, we performed high-throughput evaluation of prime editor 2 (PE2) activities in human cells using 54,836 pairs of prime editing guide RNAs (pegRNAs) and their target sequences. The resulting data sets allowed us to identify factors affecting PE2 efficiency and to develop three computational models to predict pegRNA efficiency. For a given target sequence, the computational models predict efficiencies of pegRNAs with different lengths of primer binding sites and reverse transcriptase templates for edits of various types and positions. Testing the accuracy of the predictions using test data sets that were not used for training, we found Spearman's correlations between 0.47 and 0.81. Our computational models and information about factors affecting PE2 efficiency will facilitate practical application of prime editing.
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Affiliation(s)
- Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Goosang Yu
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seonwoo Min
- Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sungtae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungroh Yoon
- Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea.
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25
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Jia X, Burugula BB, Chen V, Lemons RM, Jayakody S, Maksutova M, Kitzman JO. Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk. Am J Hum Genet 2021; 108:163-175. [PMID: 33357406 PMCID: PMC7820803 DOI: 10.1016/j.ajhg.2020.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
The lack of functional evidence for the majority of missense variants limits their clinical interpretability and poses a key barrier to the broad utility of carrier screening. In Lynch syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed “variants of uncertain significance” (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians’ interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the ∼1,300 extant missense VUSs in MSH2 and may facilitate the prospective classification of newly discovered variants in the clinic.
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26
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Klein JC, Agarwal V, Inoue F, Keith A, Martin B, Kircher M, Ahituv N, Shendure J. A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nat Methods 2020; 17:1083-1091. [PMID: 33046894 PMCID: PMC7727316 DOI: 10.1038/s41592-020-0965-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/27/2020] [Indexed: 01/02/2023]
Abstract
Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. To date, there are limited studies that systematically compare differences in MPRA design. Here, we screen a library of 2,440 candidate liver enhancers and controls for regulatory activity in HepG2 cells using nine different MPRA designs. We identify subtle but significant differences that correlate with epigenetic and sequence-level features, as well as differences in dynamic range and reproducibility. We also validate that enhancer activity is largely independent of orientation, at least for our library and designs. Finally, we assemble and test the same enhancers as 192-mers, 354-mers and 678-mers and observe sizable differences. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements and to a lesser degree the precise assay, influence MPRA results.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Aidan Keith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
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27
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Kim N, Kim HK, Lee S, Seo JH, Choi JW, Park J, Min S, Yoon S, Cho SR, Kim HH. Prediction of the sequence-specific cleavage activity of Cas9 variants. Nat Biotechnol 2020; 38:1328-1336. [PMID: 32514125 DOI: 10.1038/s41587-020-0537-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022]
Abstract
Several Streptococcus pyogenes Cas9 (SpCas9) variants have been developed to improve an enzyme's specificity or to alter or broaden its protospacer-adjacent motif (PAM) compatibility, but selecting the optimal variant for a given target sequence and application remains difficult. To build computational models to predict the sequence-specific activity of 13 SpCas9 variants, we first assessed their cleavage efficiency at 26,891 target sequences. We found that, of the 256 possible four-nucleotide NNNN sequences, 156 can be used as a PAM by at least one of the SpCas9 variants. For the high-fidelity variants, overall activity could be ranked as SpCas9 ≥ Sniper-Cas9 > eSpCas9(1.1) > SpCas9-HF1 > HypaCas9 ≈ xCas9 >> evoCas9, whereas their overall specificities could be ranked as evoCas9 >> HypaCas9 ≥ SpCas9-HF1 ≈ eSpCas9(1.1) > xCas9 > Sniper-Cas9 > SpCas9. Using these data, we developed 16 deep-learning-based computational models that accurately predict the activity of these variants at any target sequence.
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Affiliation(s)
- Nahye Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Sungtae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwa Seo
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Woo Choi
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seonwoo Min
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Sung-Rae Cho
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Graduate Program of NanoScience and Technology, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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28
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Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC. Rational Reprogramming of Cellular States by Combinatorial Perturbation. Cell Rep 2020; 27:3486-3499.e6. [PMID: 31216470 DOI: 10.1016/j.celrep.2019.05.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Ectopic expression of transcription factors (TFs) can reprogram cell state. However, because of the large combinatorial space of possible TF cocktails, it remains difficult to identify TFs that reprogram specific cell types. Here, we develop Reprogram-Seq to experimentally screen thousands of TF cocktails for reprogramming performance. Reprogram-Seq leverages organ-specific cell-atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Focusing on the cardiac system, we perform Reprogram-Seq on MEFs using an undirected library of 48 cardiac factors and, separately, a directed library of 10 epicardial-related TFs. We identify a combination of three TFs, which efficiently reprogram MEFs to epicardial-like cells that are transcriptionally, molecularly, morphologically, and functionally similar to primary epicardial cells. Reprogram-Seq holds promise to accelerate the generation of specific cell types for regenerative medicine.
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Affiliation(s)
- Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minoti Bhakta
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiqi Xie
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nikhil V Munshi
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
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29
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Davis JE, Insigne KD, Jones EM, Hastings QA, Boldridge WC, Kosuri S. Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays. Cell Syst 2020; 11:75-85.e7. [PMID: 32603702 DOI: 10.1016/j.cels.2020.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 02/16/2020] [Accepted: 05/26/2020] [Indexed: 11/15/2022]
Abstract
In eukaryotes, transcription factors (TFs) orchestrate gene expression by binding to TF-binding sites (TFBSs) and localizing transcriptional co-regulators and RNA polymerase II to cis-regulatory elements. However, we lack a basic understanding of the relationship between TFBS composition and their quantitative transcriptional responses. Here, we measured expression driven by 17,406 synthetic cis-regulatory elements with varied compositions of a model TFBS, the c-AMP response element (CRE) by using massively parallel reporter assays (MPRAs). We find CRE number, affinity, and promoter proximity largely determines expression. In addition, we observe expression modulation based on the spacing between CREs and CRE distance to the promoter, where expression follows a helical periodicity. Finally, we compare library expression between an episomal MPRA and a genomically integrated MPRA, where a single cis-regulatory element is assayed per cell at a defined locus. These assays largely recapitulate each other, although weaker, non-canonical CREs exhibit greater activity in a genomic context.
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Affiliation(s)
- Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kimberly D Insigne
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Quinn A Hastings
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - W Clifford Boldridge
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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30
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Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell 2020; 181:728-744.e21. [PMID: 32302591 PMCID: PMC7219528 DOI: 10.1016/j.cell.2020.03.039] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/13/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Adoptive transfer of genetically modified immune cells holds great promise for cancer immunotherapy. CRISPR knockin targeting can improve cell therapies, but more high-throughput methods are needed to test which knockin gene constructs most potently enhance primary cell functions in vivo. We developed a widely adaptable technology to barcode and track targeted integrations of large non-viral DNA templates and applied it to perform pooled knockin screens in primary human T cells. Pooled knockin of dozens of unique barcoded templates into the T cell receptor (TCR)-locus revealed gene constructs that enhanced fitness in vitro and in vivo. We further developed pooled knockin sequencing (PoKI-seq), combining single-cell transcriptome analysis and pooled knockin screening to measure cell abundance and cell state ex vivo and in vivo. This platform nominated a novel transforming growth factor β (TGF-β) R2-41BB chimeric receptor that improved solid tumor clearance. Pooled knockin screening enables parallelized re-writing of endogenous genetic sequences to accelerate discovery of knockin programs for cell therapies.
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Affiliation(s)
- Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - P Jonathan Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Franziska Blaeschke
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jasper F Nies
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Cody Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ruby Yu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle L T Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anna Truong
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Goodman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Kole Roybal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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31
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Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol 2020; 38:638-648. [PMID: 32249828 DOI: 10.1038/s41587-020-0437-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Systematic mapping of genetic interactions (GIs) and interrogation of the functions of sizable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR (clustered regularly interspaced short palindromic repeats)-based screening system for combinatorial genetic manipulation that employs coexpression of CRISPR-associated nucleases 9 and 12a (Cas9 and Cas12a) and machine-learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named Cas Hybrid for Multiplexed Editing and screening Applications (CHyMErA), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive GIs and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemogenetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for GI mapping and the functional analysis of sizable genomic regions, such as alternative exons.
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Affiliation(s)
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Tanja Durbic
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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32
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Matreyek KA, Stephany JJ, Chiasson MA, Hasle N, Fowler DM. An improved platform for functional assessment of large protein libraries in mammalian cells. Nucleic Acids Res 2020; 48:e1. [PMID: 31612958 PMCID: PMC7145622 DOI: 10.1093/nar/gkz910] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022] Open
Abstract
Multiplex genetic assays can simultaneously test thousands of genetic variants for a property of interest. However, limitations of existing multiplex assay methods in cultured mammalian cells hinder the breadth, speed and scale of these experiments. Here, we describe a series of improvements that greatly enhance the capabilities of a Bxb1 recombinase-based landing pad system for conducting different types of multiplex genetic assays in various mammalian cell lines. We incorporate the landing pad into a lentiviral vector, easing the process of generating new landing pad cell lines. We also develop several new landing pad versions, including one where the Bxb1 recombinase is expressed from the landing pad itself, improving recombination efficiency more than 2-fold and permitting rapid prototyping of transgenic constructs. Other versions incorporate positive and negative selection markers that enable drug-based enrichment of recombinant cells, enabling the use of larger libraries and reducing costs. A version with dual convergent promoters allows enrichment of recombinant cells independent of transgene expression, permitting the assessment of libraries of transgenes that perturb cell growth and survival. Lastly, we demonstrate these improvements by assessing the effects of a combinatorial library of oncogenes and tumor suppressors on cell growth. Collectively, these advancements make multiplex genetic assays in diverse cultured cell lines easier, cheaper and more effective, facilitating future studies probing how proteins impact cell function, using transgenic variant libraries tested individually or in combination.
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Affiliation(s)
- Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Melissa A Chiasson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Hasle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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33
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Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Res 2019; 47:7989-8003. [PMID: 31165867 PMCID: PMC6735782 DOI: 10.1093/nar/gkz487] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 12/22/2022] Open
Abstract
Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: (i) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, (ii) deletions are predominantly associated with microhomology and (iii) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording.
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Affiliation(s)
- Wei Chen
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jacob Schreiber
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Maximilian Haeussler
- Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Yi Yin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
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34
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Murray CW, Brady JJ, Tsai MK, Li C, Winters IP, Tang R, Andrejka L, Ma RK, Kunder CA, Chu P, Winslow MM. An LKB1-SIK Axis Suppresses Lung Tumor Growth and Controls Differentiation. Cancer Discov 2019; 9:1590-1605. [PMID: 31350327 PMCID: PMC6825558 DOI: 10.1158/2159-8290.cd-18-1237] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 05/09/2019] [Accepted: 07/22/2019] [Indexed: 12/29/2022]
Abstract
The kinase LKB1 is a critical tumor suppressor in sporadic and familial human cancers, yet the mechanisms by which it suppresses tumor growth remain poorly understood. To investigate the tumor-suppressive capacity of four canonical families of LKB1 substrates in vivo, we used CRISPR/Cas9-mediated combinatorial genome editing in a mouse model of oncogenic KRAS-driven lung adenocarcinoma. We demonstrate that members of the SIK family are critical for constraining tumor development. Histologic and gene-expression similarities between LKB1- and SIK-deficient tumors suggest that SIKs and LKB1 operate within the same axis. Furthermore, a gene-expression signature reflecting SIK deficiency is enriched in LKB1-mutant human lung adenocarcinomas and is regulated by LKB1 in human cancer cell lines. Together, these findings reveal a key LKB1-SIK tumor-suppressive axis and underscore the need to redirect efforts to elucidate the mechanisms through which LKB1 mediates tumor suppression. SIGNIFICANCE: Uncovering the effectors of frequently altered tumor suppressor genes is critical for understanding the fundamental driving forces of cancer growth. Our identification of the SIK family of kinases as effectors of LKB1-mediated tumor suppression will refocus future mechanistic studies and may lead to new avenues for genotype-specific therapeutic interventions.This article is highlighted in the In This Issue feature, p. 1469.
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Affiliation(s)
- Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Jennifer J Brady
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Ian P Winters
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Rosanna K Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Monte M Winslow
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California.
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
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35
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Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC. Optical Pooled Screens in Human Cells. Cell 2019; 179:787-799.e17. [PMID: 31626775 PMCID: PMC6886477 DOI: 10.1016/j.cell.2019.09.016] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 01/06/2023]
Abstract
Genetic screens are critical for the systematic identification of genes underlying cellular phenotypes. Pooling gene perturbations greatly improves scalability but is not compatible with imaging of complex and dynamic cellular phenotypes. Here, we introduce a pooled approach for optical genetic screens in mammalian cells. We use targeted in situ sequencing to demultiplex a library of genetic perturbations following image-based phenotyping. We screened a set of 952 genes across millions of cells for involvement in nuclear factor κB (NF-κB) signaling by imaging the translocation of RelA (p65) to the nucleus. Screening at a single time point across 3 cell lines recovered 15 known pathway components, while repeating the screen with live-cell imaging revealed a role for Mediator complex subunits in regulating the duration of p65 nuclear retention. These results establish a highly multiplexed approach to image-based screens of spatially and temporally defined phenotypes with pooled libraries.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Physics, MIT, Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Health Sciences and Technology, MIT, Cambridge, MA 02142, USA
| | - Anja Mezger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02142, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA.
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36
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Wang D, Zhang C, Wang B, Li B, Wang Q, Liu D, Wang H, Zhou Y, Shi L, Lan F, Wang Y. Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning. Nat Commun 2019; 10:4284. [PMID: 31537810 PMCID: PMC6753114 DOI: 10.1038/s41467-019-12281-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/24/2019] [Indexed: 12/16/2022] Open
Abstract
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/ .
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Affiliation(s)
- Daqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bei Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Qiang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Dong Liu
- Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Hongyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Feng Lan
- Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Disease, Capital Medical University, Beijing, 100029, China.
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China.
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37
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Zirin J, Ni X, Sack LM, Yang-Zhou D, Hu Y, Brathwaite R, Bulyk ML, Elledge SJ, Perrimon N. Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells. Proc Natl Acad Sci U S A 2019; 116:14614-14619. [PMID: 31262815 PMCID: PMC6642371 DOI: 10.1073/pnas.1821863116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Xiaochun Ni
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Laura M Sack
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Martha L Bulyk
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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38
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Wang C, Lu T, Emanuel G, Babcock HP, Zhuang X. Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization. Proc Natl Acad Sci U S A 2019; 116:10842-10851. [PMID: 31085639 PMCID: PMC6561216 DOI: 10.1073/pnas.1903808116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pooled-library CRISPR screening provides a powerful means to discover genetic factors involved in cellular processes in a high-throughput manner. However, the phenotypes accessible to pooled-library screening are limited. Complex phenotypes, such as cellular morphology and subcellular molecular organization, as well as their dynamics, require imaging-based readout and are currently beyond the reach of pooled-library CRISPR screening. Here we report an all imaging-based pooled-library CRISPR screening approach that combines high-content phenotype imaging with high-throughput single guide RNA (sgRNA) identification in individual cells. In this approach, sgRNAs are codelivered to cells with corresponding barcodes placed at the 3' untranslated region of a reporter gene using a lentiviral delivery system with reduced recombination-induced sgRNA-barcode mispairing. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is used to read out the barcodes and hence identify the sgRNAs with high accuracy. We used this approach to screen 162 sgRNAs targeting 54 RNA-binding proteins for their effects on RNA localization to nuclear compartments and uncovered previously unknown regulatory factors for nuclear RNA localization. Notably, our screen revealed both positive and negative regulators for the nuclear speckle localization of a long noncoding RNA, MALAT1, suggesting a dynamic regulation of lncRNA localization in subcellular compartments.
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MESH Headings
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Cell Nucleus/chemistry
- Cell Nucleus/metabolism
- Gene Editing
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Image Processing, Computer-Assisted/methods
- In Situ Hybridization, Fluorescence/methods
- Molecular Probes/chemistry
- Molecular Probes/genetics
- Molecular Probes/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Single-Cell Analysis/methods
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Affiliation(s)
- Chong Wang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
| | - Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
| | - George Emanuel
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
| | - Hazen P Babcock
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
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39
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Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Syst 2018; 7:548-555.e8. [PMID: 30448000 DOI: 10.1016/j.cels.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with single-cell RNA sequencing to assay cell state and fitness, a technique we call SEUSS (scalable functional screening by sequencing). Using SEUSS, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs) and assayed the impact of TF overexpression on fitness and transcriptomic states. We further leveraged the versatility of the ORF library approach to assay mutant genes and whole gene families. From the transcriptomic responses, we built genetic co-regulatory networks to identify altered gene modules and found that KLF4 and SNAI2 drive opposing effects along the epithelial-mesenchymal transition axis. From the fitness responses, we identified ETV2 as a driver of reprogramming toward an endothelial-like state.
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Affiliation(s)
- Udit Parekh
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dongxin Zhao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Atharv Worlikar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Neha Shah
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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40
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Wroblewska A, Dhainaut M, Ben-Zvi B, Rose SA, Park ES, Amir EAD, Bektesevic A, Baccarini A, Merad M, Rahman AH, Brown BD. Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell 2018; 175:1141-1155.e16. [PMID: 30343902 DOI: 10.1016/j.cell.2018.09.022] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/19/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters. By pairing each Pro-Code with a different CRISPR, we simultaneously analyzed multiple phenotypic markers, including phospho-signaling, on dozens of knockouts. Pro-Code/CRISPR screens found two interferon-stimulated genes, the immunoproteasome component Psmb8 and a chaperone Rtp4, are important for antigen-dependent immune editing of cancer cells and identified Socs1 as a negative regulator of Pd-l1. The Pro-Code technology enables simultaneous high-dimensional protein-level phenotyping of 100s of genes with single-cell resolution.
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Affiliation(s)
- Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Dhainaut
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin Ben-Zvi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eun Sook Park
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - El-Ad David Amir
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anela Bektesevic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alessia Baccarini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adeeb H Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Diabetes Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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41
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Starita LM, Islam MM, Banerjee T, Adamovich AI, Gullingsrud J, Fields S, Shendure J, Parvin JD. A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. Am J Hum Genet 2018; 103:498-508. [PMID: 30219179 DOI: 10.1016/j.ajhg.2018.07.016] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022] Open
Abstract
Loss-of-function pathogenic variants in BRCA1 confer a predisposition to breast and ovarian cancer. Genetic testing for sequence changes in BRCA1 frequently reveals a missense variant for which the impact on cancer risk and on the molecular function of BRCA1 is unknown. Functional BRCA1 is required for the homology-directed repair (HDR) of double-strand DNA breaks, a critical activity for maintaining genome integrity and tumor suppression. Here, we describe a multiplex HDR reporter assay for concurrently measuring the effects of hundreds of variants of BRCA1 for their role in DNA repair. Using this assay, we characterized the effects of 1,056 amino acid substitutions in the first 192 residues of BRCA1. Benchmarking these results against variants with known effects on DNA repair function or on cancer predisposition, we demonstrate accurate discrimination of loss-of-function versus benign missense variants. We anticipate that this assay can be used to functionally characterize BRCA1 missense variants at scale, even before the variants are observed in results from genetic testing.
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42
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Affiliation(s)
- Ruth E Hanna
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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43
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Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA. Mapping the Genetic Landscape of Human Cells. Cell 2018; 174:953-967.e22. [PMID: 30033366 DOI: 10.1016/j.cell.2018.06.010] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/08/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022]
Abstract
Seminal yeast studies have established the value of comprehensively mapping genetic interactions (GIs) for inferring gene function. Efforts in human cells using focused gene sets underscore the utility of this approach, but the feasibility of generating large-scale, diverse human GI maps remains unresolved. We developed a CRISPR interference platform for large-scale quantitative mapping of human GIs. We systematically perturbed 222,784 gene pairs in two cancer cell lines. The resultant maps cluster functionally related genes, assigning function to poorly characterized genes, including TMEM261, a new electron transport chain component. Individual GIs pinpoint unexpected relationships between pathways, exemplified by a specific cholesterol biosynthesis intermediate whose accumulation induces deoxynucleotide depletion, causing replicative DNA damage and a synthetic-lethal interaction with the ATR/9-1-1 DNA repair pathway. Our map provides a broad resource, establishes GI maps as a high-resolution tool for dissecting gene function, and serves as a blueprint for mapping the genetic landscape of human cells.
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Wang
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Neal K Bennett
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Chong Y Park
- Innovative Genomics Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Derek Bogdanoff
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric D Chow
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Tim R Peterson
- Department of Internal Medicine, Division of Bone and Mineral Diseases, and Department of Genetics, Institute for Public Health, Washington University School of Medicine, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Luke A Gilbert
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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44
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Xie S, Cooley A, Armendariz D, Zhou P, Hon GC. Frequent sgRNA-barcode recombination in single-cell perturbation assays. PLoS One 2018; 13:e0198635. [PMID: 29874289 PMCID: PMC5991360 DOI: 10.1371/journal.pone.0198635] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/22/2018] [Indexed: 11/18/2022] Open
Abstract
Simultaneously detecting CRISPR-based perturbations and induced transcriptional changes in the same cell is a powerful approach to unraveling genome function. Several lentiviral approaches have been developed, some of which rely on the detection of distally located genetic barcodes as an indirect proxy of sgRNA identity. Since barcodes are often several kilobases from their corresponding sgRNAs, viral recombination-mediated swapping of barcodes and sgRNAs is feasible. Using a self-circularization-based sgRNA-barcode library preparation protocol, we estimate the recombination rate to be ~50% and we trace this phenomenon to the pooled viral packaging step. Recombination is random, and decreases the signal-to-noise ratio of the assay. Our results suggest that alternative approaches can increase the throughput and sensitivity of single-cell perturbation assays.
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Affiliation(s)
- Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Anne Cooley
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Daniel Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Pei Zhou
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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45
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Hegde M, Strand C, Hanna RE, Doench JG. Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens. PLoS One 2018; 13:e0197547. [PMID: 29799876 PMCID: PMC5969736 DOI: 10.1371/journal.pone.0197547] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/03/2018] [Indexed: 12/26/2022] Open
Abstract
Many implementations of pooled screens in mammalian cells rely on linking an element of interest to a barcode, with the latter subsequently quantitated by next generation sequencing. However, substantial uncoupling between these paired elements during lentiviral production has been reported, especially as the distance between elements increases. We detail that PCR amplification is another major source of uncoupling, and becomes more pronounced with increased amounts of DNA template molecules and PCR cycles. To lessen uncoupling in systems that use paired elements for detection, we recommend minimizing the distance between elements, using low and equal template DNA inputs for plasmid and genomic DNA during PCR, and minimizing the number of PCR cycles. We also present a vector design for conducting combinatorial CRISPR screens that enables accurate barcode-based detection with a single short sequencing read and minimal uncoupling.
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Affiliation(s)
- Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christine Strand
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ruth E. Hanna
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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46
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Sack LM, Davoli T, Li MZ, Li Y, Xu Q, Naxerova K, Wooten EC, Bernardi RJ, Martin TD, Chen T, Leng Y, Liang AC, Scorsone KA, Westbrook TF, Wong KK, Elledge SJ. Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. Cell 2018; 173:499-514.e23. [PMID: 29576454 PMCID: PMC6643283 DOI: 10.1016/j.cell.2018.02.037] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 11/10/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
Abstract
Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors.
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Affiliation(s)
- Laura Magill Sack
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Teresa Davoli
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Mamie Z Li
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yuyang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Shandong Provincial Hospital affiliated to Shandong University, Jinan 250021, China
| | - Qikai Xu
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kamila Naxerova
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Eric C Wooten
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ronald J Bernardi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy D Martin
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ting Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Yumei Leng
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Anthony C Liang
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kathleen A Scorsone
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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47
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Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C. On the design of CRISPR-based single-cell molecular screens. Nat Methods 2018; 15:271-274. [PMID: 29457792 PMCID: PMC5882576 DOI: 10.1038/nmeth.4604] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/06/2018] [Indexed: 01/05/2023]
Abstract
Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
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Affiliation(s)
- Andrew J Hill
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Molly J Gasperini
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jonathan Packer
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Dana Jackson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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48
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Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC. Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nat Biotechnol 2017; 35:463-474. [PMID: 28319085 PMCID: PMC5557292 DOI: 10.1038/nbt.3834] [Citation(s) in RCA: 316] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/22/2017] [Indexed: 12/19/2022]
Abstract
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs. We applied CDKO to generate a large-scale human GI map, comprising 490,000 double-sgRNAs directed against 21,321 pairs of drug targets in K562 leukemia cells and identified synthetic lethal drug target pairs for which corresponding drugs exhibit synergistic killing. These included the BCL2L1 and MCL1 combination, which was also effective in imatinib-resistant cells. We further validated this system by identifying known and previously unidentified GIs between modifiers of ricin toxicity. This work provides an effective strategy to screen synergistic drug combinations in high-throughput and a CRISPR-based tool to dissect functional GI networks.
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Affiliation(s)
- Kyuho Han
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Edwin E. Jeng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA
| | - Gaelen T. Hess
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - David W. Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
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49
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Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell 2016; 167:1867-1882.e21. [PMID: 27984733 PMCID: PMC5315571 DOI: 10.1016/j.cell.2016.11.048] [Citation(s) in RCA: 635] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/14/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.
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Affiliation(s)
- Britt Adamson
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Norman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Y Cho
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuwen Chen
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline E Villalta
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Y Hein
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan A Pak
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew N Gray
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atray Dixit
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Oren Parnas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jonathan S Weissman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
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