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Wu Q, Wu J, Karim K, Chen X, Wang T, Iwama S, Carobbio S, Keen P, Vidal-Puig A, Kotter MR, Bassett A. Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons. Mol Cell 2023; 83:1125-1139.e8. [PMID: 36917981 PMCID: PMC10114495 DOI: 10.1016/j.molcel.2023.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 12/21/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023]
Abstract
CRISPR activation (CRISPRa) is an important tool to perturb transcription, but its effectiveness varies between target genes. We employ human pluripotent stem cells with thousands of randomly integrated barcoded reporters to assess epigenetic features that influence CRISPRa efficacy. Basal expression levels are influenced by genomic context and dramatically change during differentiation to neurons. Gene activation by dCas9-VPR is successful in most genomic contexts, including developmentally repressed regions, and activation level is anti-correlated with basal gene expression, whereas dCas9-p300 is ineffective in stem cells. Certain chromatin states, such as bivalent chromatin, are particularly sensitive to dCas9-VPR, whereas constitutive heterochromatin is less responsive. We validate these rules at endogenous genes and show that activation of certain genes elicits a change in the stem cell transcriptome, sometimes showing features of differentiated cells. Our data provide rules to predict CRISPRa outcome and highlight its utility to screen for factors driving stem cell differentiation.
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Affiliation(s)
- Qianxin Wu
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Junjing Wu
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Kaiser Karim
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Xi Chen
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Southern University of Science and Technology, 1088 Xueyuan Ave, Nanshan, Shenzhen, Guangdong 518055, China
| | - Tengyao Wang
- Department of Statistics, London School of Economics and Political Science, London WC2B 4RR, UK
| | - Sho Iwama
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Stefania Carobbio
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Metabolic Research Laboratories, Addenbrooke's Treatment Center, Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK; Centro de Investigacion Principe Felipe, 46012 Valencia, Spain
| | - Peter Keen
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Antonio Vidal-Puig
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Metabolic Research Laboratories, Addenbrooke's Treatment Center, Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK; Centro de Investigacion Principe Felipe, 46012 Valencia, Spain
| | - Mark R Kotter
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Andrew Bassett
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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Yang A, Beheshti M, Hudson TE, Vedanthan R, Riewpaiboon W, Mongkolwat P, Feng C, Rizzo JR. UNav: An Infrastructure-Independent Vision-Based Navigation System for People with Blindness and Low Vision. Sensors (Basel) 2022; 22:8894. [PMID: 36433501 PMCID: PMC9696753 DOI: 10.3390/s22228894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Vision-based localization approaches now underpin newly emerging navigation pipelines for myriad use cases, from robotics to assistive technologies. Compared to sensor-based solutions, vision-based localization does not require pre-installed sensor infrastructure, which is costly, time-consuming, and/or often infeasible at scale. Herein, we propose a novel vision-based localization pipeline for a specific use case: navigation support for end users with blindness and low vision. Given a query image taken by an end user on a mobile application, the pipeline leverages a visual place recognition (VPR) algorithm to find similar images in a reference image database of the target space. The geolocations of these similar images are utilized in a downstream task that employs a weighted-average method to estimate the end user's location. Another downstream task utilizes the perspective-n-point (PnP) algorithm to estimate the end user's direction by exploiting the 2D-3D point correspondences between the query image and the 3D environment, as extracted from matched images in the database. Additionally, this system implements Dijkstra's algorithm to calculate a shortest path based on a navigable map that includes the trip origin and destination. The topometric map used for localization and navigation is built using a customized graphical user interface that projects a 3D reconstructed sparse map, built from a sequence of images, to the corresponding a priori 2D floor plan. Sequential images used for map construction can be collected in a pre-mapping step or scavenged through public databases/citizen science. The end-to-end system can be installed on any internet-accessible device with a camera that hosts a custom mobile application. For evaluation purposes, mapping and localization were tested in a complex hospital environment. The evaluation results demonstrate that our system can achieve localization with an average error of less than 1 m without knowledge of the camera's intrinsic parameters, such as focal length.
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Affiliation(s)
- Anbang Yang
- Department of Mechanical and Aerospace Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Mahya Beheshti
- Department of Mechanical and Aerospace Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Rehabilitation Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Todd E. Hudson
- Department of Rehabilitation Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rajesh Vedanthan
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Wachara Riewpaiboon
- Department of Academic Services, Ratchasuda College, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Pattanasak Mongkolwat
- Faculty of Information and Communication Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Chen Feng
- Department of Mechanical and Aerospace Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - John-Ross Rizzo
- Department of Mechanical and Aerospace Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Rehabilitation Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
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González-Álvarez JL, Santos-Hermoso J, Soldino V, Carbonell-Vayá EJ. Male Perpetrators of Intimate Partner Violence Against Women: A Spanish Typology. J Interpers Violence 2022; 37:NP11761-NP11790. [PMID: 33637002 DOI: 10.1177/0886260521997442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Typological approaches in research of intimate partner violence against women (IPVAW) have been discussed on the basis of their validity and applicability in professional practice; yet most of the published studies on offender typologies are limited due to the use of relatively small, non-representative samples. The current study explored typologies of IPVAW perpetrators in a large-scale representative Spanish sample (n = 9,731 cases extracted from the Comprehensive Monitoring System of Gender-Based Violence Cases; VioGén System), according to classic batterer typologies proposed by Holtzworth-Munroe and Stuart (1994). To this end, the risk factors measured by the most extended Spanish police recidivism risk assessment tool (Valoración Policial del Riesgo; VPR) were used as clustering variables. Multiple correspondence analyses revealed the appropriateness of a bi-dimensional model to conceptualize IPVAW offender typologies. Our four-group solution may be described based on the levels of instability and antisociality of IPVAW offenders, as objectively measured by VPR5.0 risk indicators. Statistically significant differences between the IPVAW suggested typologies were found on all indicators, except for the presence of perpetrators younger than 24 years old and the presence of bidirectional intimate partner violence, which were equally distributed across the four groups. High instability/low antisociality (HiLa) and high instability/high antisociality (HiHa) individuals shared most risk indicators related to the aggressor's psychological instability; whereas HiHa and low instability/high antisociality (LiHa) men endorsed more antisociality indicators than statistically expected. The low instability/low antisociality (LiLa) group was characterized by the less presence of VPR risk indicators. Although the four subtypes identified in our study resembled classic typologies, we propose a new subtype, with high levels of instability and antisociality (i.e., HiHa). This work contributes to existing knowledge of the heterogeneity of these men, by providing useful typologies that can help inform prevention and treatment.
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Affiliation(s)
- José Luis González-Álvarez
- Cabinet for Coordination and Studies, Secretary of State for Security. Ministry for Home Affairs, Spain
- Institute of Forensic and Security Sciences. Autonomous University of Madrid (UAM), Spain
| | - Jorge Santos-Hermoso
- Department of Biological and Health Psychology, School of Psychology. Autonomous University of Madrid (UAM), Spain
| | - Virginia Soldino
- University Research Institute of Criminology and Criminal Science. University of Valencia, Spain
| | - Enrique J Carbonell-Vayá
- University Research Institute of Criminology and Criminal Science. University of Valencia, Spain
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Strezoska Ž, Dickerson SM, Maksimova E, Chou E, Gross MM, Hemphill K, Hardcastle T, Perkett M, Stombaugh J, Miller GW, Anderson EM, Vermeulen A, Smith AVB. CRISPR-mediated transcriptional activation with synthetic guide RNA. J Biotechnol 2020; 319:25-35. [PMID: 32470463 DOI: 10.1016/j.jbiotec.2020.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 04/03/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
The CRISPR-Cas9 system has been adapted for transcriptional activation (CRISPRa) and several second-generation CRISPRa systems (including VPR, SunTag, and SAM) have been developed to recruit different transcriptional activators to a deactivated Cas9, which is guided to a transcriptional start site via base complementarity with a target guide RNA. Multiple studies have shown the benefit of CRISPRa using plasmid or lentiviral expressed guide RNA, but the use of synthetic guide RNA has not been reported. Here we demonstrate the effective use of synthetic guide RNA for gene activation via CRISPRa. CRISPRa crRNA may be used with a canonical tracrRNA using the VPR or SunTag activation systems or with an extended tracrRNA containing an aptamer sequence for the SAM system. Transcriptional activation with synthetic crRNA:tracrRNA is comparable to activation achieved with expression vectors and combining several crRNA sequences targeting the same gene can enhance transcriptional activation. The use of synthetic crRNA is also ideal for simultaneous activation of multiple genes or use with dCas9-VPR mRNA when viral transduction is not feasible. Here, we perform a proof-of-principle arrayed screen using a CRISPRa crRNA library consisting of 153 cytokine receptor targets to identify regulators of IL-6 cytokine secretion. Together, these results demonstrate the suitability of synthetic CRISPRa guide RNA for high throughput, arrayed screening applications which allow for more complex phenotypic readouts to complement viability and drug resistance assays typically used in a pooled screening format.
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Affiliation(s)
| | | | | | - Eldon Chou
- Horizon Discovery, Lafayette 80026, United States
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Wang XG, Ma SY, Chang JS, Shi R, Wang RL, Zhao P, Xia QY. Programmable activation of Bombyx gene expression using CRISPR/dCas9 fusion systems. Insect Sci 2019; 26:983-990. [PMID: 30088341 DOI: 10.1111/1744-7917.12634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have made it possible to reprogram target gene expression without cloning complementary DNA or disturbing genomic sequence in mammalian cells and several multicellular organisms. We previously showed that CRISPR-associated protein 9 (Cas9) and CRISPR from Prevotella and Francisella 1 (Cpf1) could induce target mutations, deletions, inversions, and duplications both singly and multiplex in silkworm, Bombyx mori. However, it remains unknown whether the CRISPR activation (CRISPRa) system can be used in B. mori. In this study, we investigated the CRISPRa system, in which a nuclease dead Streptococcus pyogenes Cas9 (SpCas9) is fused to two transcription activation domains, including VP64 (a tetramer of the herpes simplex VP16 transcriptional activator domain), and VPR (a tripartite activator, composed of VP64, p65, and Rta). The results showed that both dCas9-VP64 and dCas9-VPR systems could be used in B. mori cells, of which the latter showed significantly higher activity. The dCas9-VPR system showed considerable activity on all five tested target genes, and further analysis revealed that the up-regulation of genes was negatively correlated to their basal expression level. We also observed that this system could be used to upregulate a range of target genes. Taken together, our findings demonstrate that CRISPRa can be a powerful tool to study gene functions in B. mori and perhaps other non-drosophila insects.
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Affiliation(s)
- Xiao-Gang Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - San-Yuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Jia-Song Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Run Shi
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ruo-Lin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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Abstract
Nuclease dead Cas9 (dCas9) has been widely used for modulating gene expression by fusing with different activation or repression domains. However, delivery of the CRISPR/Cas system fused with various effector domains in a single adeno-associated virus (AAV) remains challenging due to the payload limit. Here, we engineered a set of downsized variants of Cas9 including Staphylococcus aureus Cas9 (SaCas9) that retained DNA binding activity by deleting conserved functional domains. We demonstrated that fusing FokI nuclease domain to the N-terminal of the minimal SaCas9 (mini-SaCas9) or to the middle of the split mini-SaCas9 can trigger efficient DNA cleavage. In addition, we constructed a set of compact transactivation domains based on the tripartite VPR activation domain and self-assembled arrays of split SpyTag:SpyCatch peptides, which are suitable for fusing to the mini-SaCas9. Lastly, we produced a single AAV containing the mini-SaCas9 fused with a downsized transactivation domain along with an optimized gRNA expression cassette, which showed efficient transactivation activity. Our results highlighted a practical approach to generate down-sized CRISPR/Cas9 and gene activation systems for in vivo applications.
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Affiliation(s)
- Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Tsinghua National Lab for Information Science and Technology , Tsinghua University , Beijing 100084 , China
| | - Shuguang Peng
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Tsinghua National Lab for Information Science and Technology , Tsinghua University , Beijing 100084 , China
| | - Weiren Huang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology , Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University , Shenzhen , China
| | - Zhiming Cai
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology , Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University , Shenzhen , China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Tsinghua National Lab for Information Science and Technology , Tsinghua University , Beijing 100084 , China
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Jensen ED, Ferreira R, Jakočiūnas T, Arsovska D, Zhang J, Ding L, Smith JD, David F, Nielsen J, Jensen MK, Keasling JD. Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies. Microb Cell Fact 2017; 16:46. [PMID: 28298224 PMCID: PMC5353793 DOI: 10.1186/s12934-017-0664-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/11/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Transcriptional reprogramming is a fundamental process of living cells in order to adapt to environmental and endogenous cues. In order to allow flexible and timely control over gene expression without the interference of native gene expression machinery, a large number of studies have focused on developing synthetic biology tools for orthogonal control of transcription. Most recently, the nuclease-deficient Cas9 (dCas9) has emerged as a flexible tool for controlling activation and repression of target genes, by the simple RNA-guided positioning of dCas9 in the vicinity of the target gene transcription start site. RESULTS In this study we compared two different systems of dCas9-mediated transcriptional reprogramming, and applied them to genes controlling two biosynthetic pathways for biobased production of isoprenoids and triacylglycerols (TAGs) in baker's yeast Saccharomyces cerevisiae. By testing 101 guide-RNA (gRNA) structures on a total of 14 different yeast promoters, we identified the best-performing combinations based on reporter assays. Though a larger number of gRNA-promoter combinations do not perturb gene expression, some gRNAs support expression perturbations up to ~threefold. The best-performing gRNAs were used for single and multiplex reprogramming strategies for redirecting flux related to isoprenoid production and optimization of TAG profiles. From these studies, we identified both constitutive and inducible multiplex reprogramming strategies enabling significant changes in isoprenoid production and increases in TAG. CONCLUSION Taken together, we show similar performance for a constitutive and an inducible dCas9 approach, and identify multiplex gRNA designs that can significantly perturb isoprenoid production and TAG profiles in yeast without editing the genomic context of the target genes. We also identify a large number of gRNA positions in 14 native yeast target pomoters that do not affect expression, suggesting the need for further optimization of gRNA design tools and dCas9 engineering.
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Affiliation(s)
- Emil D. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Dushica Arsovska
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jie Zhang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Ling Ding
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Justin D. Smith
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Stanford Genome Technology Center, Palo Alto, CA 94304 USA
| | - Florian David
- Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jay D. Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA USA
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