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Li HD, Ma PQ, Wang JY, Yin BC, Ye BC. A DNA Nanodevice-Based Platform with Diverse Capabilities. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302301. [PMID: 37140089 DOI: 10.1002/smll.202302301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/21/2023] [Indexed: 05/05/2023]
Abstract
Social biotic colonies often perform intricate tasks by interindividual communication and cooperation. Inspired by these biotic behaviors, a DNA nanodevice community is proposed as a universal and scalable platform. The modular nanodevice as the infrastructure of platform contains a DNA origami triangular prism framework and a hairpin-swing arm machinery core. By coding and decoding a signal domain on the shuttled output strand in different nanodevices, an orthogonal inter-nanodevice communication network is established to connect multi-nanodevices into a functional platform. The nanodevice platform enables implementation of diverse tasks, including signal cascading and feedback, molecular input recording, distributed logic computing, and modeling of simulation for virus transmission. The nanodevice platform with powerful compatibility and programmability presents an elegant example of the combination of the distributed operation of multiple devices and the complicated interdevice communication network, and may become a new generation of intelligent DNA nanosystems.
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Affiliation(s)
- Hua-Dong Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Pei-Qiang Ma
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jin-Yu Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang, 832000, China
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Lear SK, Shipman SL. Molecular recording: transcriptional data collection into the genome. Curr Opin Biotechnol 2023; 79:102855. [PMID: 36481341 PMCID: PMC10547096 DOI: 10.1016/j.copbio.2022.102855] [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: 05/31/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Advances in regenerative medicine depend upon understanding the complex transcriptional choreography that guides cellular development. Transcriptional molecular recorders, tools that record different transcriptional events into the genome of cells, hold promise to elucidate both the intensity and timing of transcriptional activity at single-cell resolution without requiring destructive multitime point assays. These technologies are dependent on DNA writers, which translate transcriptional signals into stable genomic mutations that encode the duration, intensity, and order of transcriptional events. In this review, we highlight recent progress toward more informative and multiplexable transcriptional recording through the use of three different types of DNA writing - recombineering, Cas1-Cas2 acquisition, and prime editing - and the architecture of the genomic data generated.
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Affiliation(s)
- Sierra K Lear
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Samarth N, Gulhane P, Singh S. Immunoregulatory framework and the role of miRNA in the pathogenesis of NSCLC - A systematic review. Front Oncol 2022; 12:1089320. [PMID: 36620544 PMCID: PMC9811680 DOI: 10.3389/fonc.2022.1089320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
With a 5-year survival rate of only 15%, non-small cell lung cancer (NSCLC), the most common kind of lung carcinoma and the cause of millions of deaths annually, has drawn attention. Numerous variables, such as disrupted signaling caused by somatic mutations in the EGFR-mediated RAS/RAF/MAPK, PI3K/AKT, JAK/STAT signaling cascade, supports tumour survival in one way or another. Here, the tumour microenvironment significantly contributes to the development of cancer by thwarting the immune response. MicroRNAs (miRNAs) are critical regulators of gene expression that can function as oncogenes or oncosuppressors. They have a major influence on the occurrence and prognosis of NSCLC. Though, a myriad number of therapies are available and many are being clinically tested, still the drug resistance, its adverse effect and toxicity leading towards fatality cannot be ruled out. In this review, we tried to ascertain the missing links in between perturbed EGFR signaling, miRNAs favouring tumorigenesis and the autophagy mechanism. While connecting all the aforementioned points multiple associations were set, which can be targeted in order to combat NSCLC. Here, we tried illuminating designing synthetically engineered circuits with the toggle switches that might lay a prototype for better therapeutic paradigm.
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Affiliation(s)
| | | | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune, India
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Schmidt F, Zimmermann J, Tanna T, Farouni R, Conway T, Macpherson AJ, Platt RJ. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 2022; 376:eabm6038. [PMID: 35549411 PMCID: PMC11163514 DOI: 10.1126/science.abm6038] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.
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Affiliation(s)
- Florian Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Tanmay Tanna
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, 8092 Zurich, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Andrew J. Macpherson
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
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Gohil N, Bhattacharjee G, Lam NL, Perli SD, Singh V. CRISPR-Cas systems: Challenges and future prospects. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:141-151. [PMID: 33934835 DOI: 10.1016/bs.pmbts.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The advancement gained over the past couple of decades in clustered regularly interspaced short palindromic repeats and CRISPR associated proteins (CRISPR-Cas) systems have revolutionized the field of synthetic biology, therapeutics, diagnostics and metabolic engineering. The technique has enabled the process of genome editing to be very precise, rapid, cost-effective and highly efficient which were the downfalls for the previously debuted zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) technologies. However, despite its great potential, challenges including off-target activity, method of delivery, ethical and regulatory issues still remain unresolved for the CRISPR-Cas systems. In this chapter, we present and point out the obstacles faced in implementation of the CRISPR-Cas system along with its future prospects.
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Affiliation(s)
- Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Samuel D Perli
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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Brown W, Zhou W, Deiters A. Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control. Chembiochem 2021; 22:63-72. [PMID: 32833316 PMCID: PMC7928076 DOI: 10.1002/cbic.202000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Indexed: 12/26/2022]
Abstract
Conditional control of CRISPR/Cas9 has been developed by using a variety of different approaches, many focusing on manipulation of the Cas9 protein itself. However, more recent strategies for governing CRISPR/Cas9 function are based on guide RNA (gRNA) modifications. They include control of gRNAs by light, small molecules, proteins, and oligonucleotides. These designs have unique advantages compared to other approaches and have allowed precise regulation of gene editing and transcription. Here, we discuss strategies for conditional control of gRNA function and compare effectiveness of these methods.
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Affiliation(s)
| | | | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (USA)
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Tanna T, Schmidt F, Cherepkova MY, Okoniewski M, Platt RJ. Recording transcriptional histories using Record-seq. Nat Protoc 2020; 15:513-539. [DOI: 10.1038/s41596-019-0253-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/08/2019] [Indexed: 01/17/2023]
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8
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Katayama K, Mitsunobu H, Nishida K. Mammalian synthetic biology by CRISPRs engineering and applications. Curr Opin Chem Biol 2019; 52:79-84. [DOI: 10.1016/j.cbpa.2019.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 10/26/2022]
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Campa CC, Weisbach NR, Santinha AJ, Incarnato D, Platt RJ. Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods 2019; 16:887-893. [PMID: 31406383 DOI: 10.1038/s41592-019-0508-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022]
Abstract
The ability to modify multiple genetic elements simultaneously would help to elucidate and control the gene interactions and networks underlying complex cellular functions. However, current genome engineering technologies are limited in both the number and the type of perturbations that can be performed simultaneously. Here, we demonstrate that both Cas12a and a clustered regularly interspaced short palindromic repeat (CRISPR) array can be encoded in a single transcript by adding a stabilizer tertiary RNA structure. By leveraging this system, we illustrate constitutive, conditional, inducible, orthogonal and multiplexed genome engineering of endogenous targets using up to 25 individual CRISPR RNAs delivered on a single plasmid. Our method provides a powerful platform to investigate and orchestrate the sophisticated genetic programs underlying complex cell behaviors.
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Affiliation(s)
- Carlo C Campa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Niels R Weisbach
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - António J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Department of Chemistry, University of Basel, Basel, Switzerland.
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Plant virus-based materials for biomedical applications: Trends and prospects. Adv Drug Deliv Rev 2019; 145:96-118. [PMID: 30176280 DOI: 10.1016/j.addr.2018.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022]
Abstract
Nanomaterials composed of plant viral components are finding their way into medical technology and health care, as they offer singular properties. Precisely shaped, tailored virus nanoparticles (VNPs) with multivalent protein surfaces are efficiently loaded with functional compounds such as contrast agents and drugs, and serve as carrier templates and targeting vehicles displaying e.g. peptides and synthetic molecules. Multiple modifications enable uses including vaccination, biosensing, tissue engineering, intravital delivery and theranostics. Novel concepts exploit self-organization capacities of viral building blocks into hierarchical 2D and 3D structures, and their conversion into biocompatible, biodegradable units. High yields of VNPs and proteins can be harvested from plants after a few days so that various products have reached or are close to commercialization. The article delineates potentials and limitations of biomedical plant VNP uses, integrating perspectives of chemistry, biomaterials sciences, molecular plant virology and process engineering.
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Schmidt F, Cherepkova MY, Platt RJ. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 2018; 562:380-385. [DOI: 10.1038/s41586-018-0569-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022]
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