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Yuan S, Bremmer A, Yang X, Li J, Hu Q. Splittable systems in biomedical applications. Biomater Sci 2024; 12:4103-4116. [PMID: 39012216 DOI: 10.1039/d4bm00709c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Splittable systems have emerged as a powerful approach for the precise spatiotemporal control of biological processes. This concept relies on splitting a functional molecule into inactive fragments, which can be reassembled under specific conditions or stimuli to regain activity. Several binding pairs and orthogonal split fragments are introduced by fusing with other modalities to develop more complex and robust designs. One of the pillars of these splittable systems is modularity, which involves decoupling targeting, activation, and effector functions. Challenges, such as off-target effects and overactivation, can be addressed through precise control. This review provides an overview of the design principles, strategies, and applications of splittable systems across diverse fields including immunotherapy, gene editing, prodrug activation, biosensing, and synthetic biology.
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Affiliation(s)
- Sichen Yuan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
| | - Alexa Bremmer
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Xicheng Yang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Jiayue Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
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Chai W, Hao W, Liu J, Han Z, Chang S, Cheng L, Sun M, Yan G, Liu Z, Liu Y, Zhang G, Xing L, Chen H, Liu P. Visualizing Cathepsin K-Cre Expression at the Single-Cell Level with GFP Reporters. JBMR Plus 2022; 7:e10706. [PMID: 36699636 PMCID: PMC9850439 DOI: 10.1002/jbm4.10706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The Cre/lox system is a fundamental tool for functional genomic studies, and a number of Cre lines have been generated to target genes of interest spatially and temporally in defined cells or tissues; this approach has greatly expanded our knowledge of gene functions. However, the limitations of this system have recently been recognized, and we must address the challenge of so-called nonspecific/off-target effects when a Cre line is utilized to investigate a gene of interest. For example, cathepsin K (Ctsk) has been used as a specific osteoclast marker, and Cre driven by its promoter is widely utilized for osteoclast investigations. However, Ctsk-Cre expression has recently been identified in other cell types, such as osteocytes, periosteal stem cells, and tenocytes. To better understand Ctsk-Cre expression and ensure appropriate use of this Cre line, we performed a comprehensive analysis of Ctsk-Cre expression at the single-cell level in major organs and tissues using two green fluorescent protein (GFP) reporters (ROSA nT-nG and ROSA tdT) and a tissue clearing technique in young and aging mice. The expression profile was further verified by immunofluorescence staining and droplet digital RT-PCR. The results demonstrate that Ctsk-Cre is expressed not only in osteoclasts but also at various levels in osteoblast lineage cells and other major organs/tissues, particularly in the brain, kidney, pancreas, and blood vessels. Furthermore, Ctsk-Cre expression increases markedly in the bone marrow, skeletal muscle, and intervertebral discs in aging mice. These data will be valuable for accurately interpreting data obtained from in vivo studies using Ctsk-Cre mice to avoid potentially misleading conclusions. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Wenhuan Chai
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Weiwei Hao
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Jintao Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Zhenglin Han
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Shiyu Chang
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Liben Cheng
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Mingxin Sun
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Guofang Yan
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Zemin Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Yin Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Guodong Zhang
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Li Xing
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Hongqian Chen
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Peng Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
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Kroning KE, Wang W. Temporally gated molecular tools for tracking protein-protein interactions in live cells. Methods Enzymol 2020; 640:205-223. [PMID: 32560799 DOI: 10.1016/bs.mie.2020.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Protein-protein interactions (PPIs) are essential in most biological processes. Even though many methods were designed to detect PPIs, detecting PPIs in a large volume of cells with a temporal resolution remains challenging. Recent development of light gated transcriptional reporters, such as SPARK and iTANGO, enabled detection of PPI in a large population of cells with a temporal resolution on the order of minutes. In this chapter, we discussed in detail the application of SPARK to detect PPIs between the activated β-2 adrenergic receptor (B2AR) and both Gα mimic and β-arrestin2. Because SPARK is a multi-component system, the protein expression level is critical for its optimal performance. We also discussed the detailed protocols for using SPARK with either transfection or lentiviral infection in HEK296T/17 cells.
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Affiliation(s)
- Kayla E Kroning
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Wenjing Wang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States.
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Abstract
Optogenetic tools can provide direct and programmable control of gene expression. Light-inducible recombinases, in particular, offer a powerful method for achieving precise spatiotemporal control of DNA modification. However, to-date this technology has been largely limited to eukaryotic systems. Here, we develop optogenetic recombinases for Escherichia coli that activate in response to blue light. Our approach uses a split recombinase coupled with photodimers, where blue light brings the split protein together to form a functional recombinase. We tested both Cre and Flp recombinases, Vivid and Magnet photodimers, and alternative protein split sites in our analysis. The optimal configuration, Opto-Cre-Vvd, exhibits strong blue light-responsive excision and low ambient light sensitivity. For this system we characterize the effect of light intensity and the temporal dynamics of light-induced recombination. These tools expand the microbial optogenetic toolbox, offering the potential for precise control of DNA excision with light-inducible recombinases in bacteria.
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Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Wilson W Wong
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Mary J Dunlop
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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Wink M. Editorial: Biotechnology Journal's diverse coverage of biotechnology. Biotechnol J 2014; 9:311-2. [PMID: 24591238 DOI: 10.1002/biot.201300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This issue of Biotechnology Journal is a regular issue edited by Prof. Michael Wink. The issue covers all the major focus areas of the journal, including medical biotechnology, synthetic biology, and novel biotechnological methods.
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Affiliation(s)
- Michael Wink
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Heidelberg, Germany.
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