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Přibylová A, Fischer L. How to use CRISPR/Cas9 in plants: from target site selection to DNA repair. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5325-5343. [PMID: 38648173 PMCID: PMC11389839 DOI: 10.1093/jxb/erae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/21/2024] [Indexed: 04/25/2024]
Abstract
A tool for precise, target-specific, efficient, and affordable genome editing is a dream for many researchers, from those who conduct basic research to those who use it for applied research. Since 2012, we have tool that almost fulfils such requirements; it is based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems. However, even CRISPR/Cas has limitations and obstacles that might surprise its users. In this review, we focus on the most frequently used variant, CRISPR/Cas9 from Streptococcus pyogenes, and highlight key factors affecting its mutagenesis outcomes: (i) factors affecting the CRISPR/Cas9 activity, such as the effect of the target sequence, chromatin state, or Cas9 variant, and how long it remains in place after cleavage; and (ii) factors affecting the follow-up DNA repair mechanisms including mostly the cell type and cell cycle phase, but also, for example, the type of DNA ends produced by Cas9 cleavage (blunt/staggered). Moreover, we note some differences between using CRISPR/Cas9 in plants, yeasts, and animals, as knowledge from individual kingdoms is not fully transferable. Awareness of these factors can increase the likelihood of achieving the expected results of plant genome editing, for which we provide detailed guidelines.
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Affiliation(s)
- Adéla Přibylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
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2
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Vollen K, Zhao C, Alonso JM, Stepanova AN. Sourcing DNA parts for synthetic biology applications in plants. Curr Opin Biotechnol 2024; 87:103140. [PMID: 38723389 DOI: 10.1016/j.copbio.2024.103140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024]
Abstract
Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.
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Affiliation(s)
- Katie Vollen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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3
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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4
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Jiang Q, Geng F, Shen J, Zhu P, Lu Z, Lu F, Zhou L. Blue light-mediated gene expression as a promising strategy to reduce antibiotic resistance in Escherichia coli. Biotechnol J 2024; 19:e2400023. [PMID: 38719589 DOI: 10.1002/biot.202400023] [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: 01/10/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 08/21/2024]
Abstract
The discovery of antibiotics has noticeably promoted the development of human civilization; however, antibiotic resistance in bacteria caused by abusing and overusing greatly challenges human health and food safety. Considering the worsening situation, it is an urgent demand to develop emerging nontraditional technologies or methods to address this issue. With the expanding of synthetic biology, optogenetics exhibits a tempting prospect for precisely regulating gene expression in many fields. Consequently, it is attractive to employ optogenetics to reduce the risk of antibiotic resistance. Here, a blue light-controllable gene expression system was established in Escherichia coli based on a photosensitive DNA-binding protein (EL222). Further, this strategy was successfully applied to repress the expression of β-lactamase gene (bla) using blue light illumination, resulting a dramatic reduction of ampicillin resistance in engineered E. coli. Moreover, blue light was utilized to induce the expression of the mechanosensitive channel of large conductance (MscL), triumphantly leading to the increase of streptomycin susceptibility in engineered E. coli. Finally, the increased susceptibility of ampicillin and streptomycin was simultaneously induced by blue light in the same E. coli cell, revealing the excellent potential of this strategy in controlling multidrug-resistant (MDR) bacteria. As a proof of concept, our work demonstrates that light can be used as an alternative tool to prolong the use period of common antibiotics without developing new antibiotics. And this novel strategy based on optogenetics shows a promising foreground to combat antibiotic resistance in the future.
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Affiliation(s)
- Qingwei Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Feng Geng
- College of Pharmacy, Binzhou Medical University, Yantai, PR China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
| | - Libang Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, PR China
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5
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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6
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Liang Z, Wei S, Wu Y, Guo Y, Zhang B, Yang H. Temporally gene knockout using heat shock-inducible genome-editing system in plants. THE PLANT GENOME 2023; 16:e20376. [PMID: 37529831 DOI: 10.1002/tpg2.20376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/22/2023] [Accepted: 07/23/2023] [Indexed: 08/03/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) has emerged as a powerful tool to generate targeted loss-of-function mutations for functional genomic studies. As a next step, tools to generate genome modifications in a spatially and temporally precise manner will enable researchers to further dissect gene function. Here, we present two heat shock-inducible genome-editing (IGE) systems that efficiently edit target genes when the system is induced, thus allowing us to target specific developmental stages. For this conditional editing system, we chose the natural heat-inducible promoter from heat-shock protein 18.2 (HSP18.2) from Arabidopsis thaliana and the synthetic heat-inducible promoter heat shock-response element HSE-COR15A to drive the expression of Cas9. We tested these two IGE systems in Arabidopsis using cyclic or continuous heat-shock treatments at the seedling and bolting stages. A real-time quantitative polymerase chain reaction analysis revealed that the HSP18.2 IGE system exhibited higher Cas9 expression levels than the HSE-COR15A IGE system upon both cyclic and continuous treatments. By targeting brassinosteroid-insensitive 1 (BRI1) and phytoene desaturase (PDS), we demonstrate that both cyclic and continuous heat inductions successfully activated the HSP18.2 IGE system at the two developmental stages, resulting in highly efficient targeted mutagenesis and clear phenotypic outcomes. By contrast, the HSE-COR15A IGE system was only induced at the seedling stage and was less effective than the HSP18.2 IGE system in terms of mutagenesis frequencies. The presented heat shock-IGE systems can be conditionally induced to efficiently inactivate genes at any developmental stage and are uniquely suited for the dissection and systematic characterization of essential genes.
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Affiliation(s)
- Zhen Liang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Sha Wei
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Yuqing Wu
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Yingjie Guo
- Research Institute of Big Data Science and Industry, Shanxi University, Taiyuan, Shanxi, China
| | - Ben Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Honghu Yang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
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7
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Koukara J, Papadopoulou KK. Advances in plant synthetic biology approaches to control expression of gene circuits. Biochem Biophys Res Commun 2023; 654:55-61. [PMID: 36889035 DOI: 10.1016/j.bbrc.2023.02.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.
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Affiliation(s)
- Jenny Koukara
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
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8
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Evangelene Christy SM, Arun V. Isolation, cloning and functional analysis of a putative constitutive promoter of E3 ubiquitin- protein ligase RF4 from Coleus amboinicus Lour. Biotechnol Appl Biochem 2022; 70:746-760. [PMID: 35931417 DOI: 10.1002/bab.2395] [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: 03/07/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022]
Abstract
Promoter is a region in the genome sequence located upstream of the transcription start site comprising cis acting elements, which initiates and regulates the transcription of an associated gene. As the need for genetically engineered plants has widened, the requirement to develop methods to optimize the control of transgene expression has also increased. Therefore, analyzing the functionality of the promoter is very important in understanding the target gene expression. The widespread use of viral constitutive promoters (Cauliflower mosaic virus - CaMV35) has raised concerns about the safety and containment of the transgene in the environment. Hence isolation and characterization of novel promoters using fast and efficient genetic engineering tools is the need of the hour. The present study, for the first time, describes the isolation and characterization of a novel constitutive promoter driving Ubiquitin E3 ligase from the plant Coleus amboinicus, a perennial herb, of Lamiaceae family. The functionality of the isolated promoter was demonstrated using the β Glucuronidase as a reporter in tobacco var Petit havana. Development of blue color in the tobacco leaves indicated the presence of a functional promoter. We describe for the first time the isolation and characterization of E3 ubiquitin- protein ligase RF4 promoter from Coleus amboinicus Lour. In silico analysis revealed the presence of core promoter elements and other responsive elements in the promoter. The functionality of the promoter was demonstrated in tobacco leaf discs via GUS staining. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- S M Evangelene Christy
- Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - V Arun
- Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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9
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Emiliani V, Entcheva E, Hedrich R, Hegemann P, Konrad KR, Lüscher C, Mahn M, Pan ZH, Sims RR, Vierock J, Yizhar O. Optogenetics for light control of biological systems. NATURE REVIEWS. METHODS PRIMERS 2022; 2:55. [PMID: 37933248 PMCID: PMC10627578 DOI: 10.1038/s43586-022-00136-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 11/08/2023]
Abstract
Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.
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Affiliation(s)
- Valentina Emiliani
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, USA
| | - Rainer Hedrich
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kai R. Konrad
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Lüscher
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Department of Clinical Neurosciences, Geneva University Hospital, Geneva, Switzerland
| | - Mathias Mahn
- Department of Neurobiology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zhuo-Hua Pan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ruth R. Sims
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Neuroscience Research Center, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Ofer Yizhar
- Departments of Brain Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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Orlov YL, Ivanisenko VA, Dobrovolskaya OB, Chen M. Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics. Int J Mol Sci 2022; 23:ijms23126759. [PMID: 35743200 PMCID: PMC9223720 DOI: 10.3390/ijms23126759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications as it was discussed at series of recent bioinformatics conferences [...].
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Affiliation(s)
- Yuriy L. Orlov
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia;
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
- Correspondence:
| | | | - Oxana B. Dobrovolskaya
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia;
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
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