1
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Dong K, Zhang W, Hu H, Cheng S, Mu Y, Yan B, Shu W, Li L, Wang H, Xiao X. A sensitive and specific nano-vehicle based on self-amplified dual-input synthetic gene circuit for intracellular imaging and treatment. Biosens Bioelectron 2022; 218:114746. [DOI: 10.1016/j.bios.2022.114746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/25/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
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2
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Yang Y, Luo T, He Y, Deng Z, Li J, Liu H, Nie J, Wang D, Huang J, Zhong S. Nanoflare Couple: Multiplexed mRNA Imaging and Logic-Controlled Combinational Therapy. Anal Chem 2022; 94:12204-12212. [PMID: 36007146 DOI: 10.1021/acs.analchem.2c02689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theranostics, which combines both diagnostic and therapeutic capabilities in one dose, has always been an intractable challenge in personalized cancer treatment. Herein, a versatile nanotheranostic platform "nanoflare couple (NC)" has been developed for in situ multiplex cancer-related mRNA imaging and subsequent logic-controlled aggregation of gold nanoparticles, leading to gene therapy and photothermal therapy upon irradiation with infrared light. As a proof of concept, TK1 and survivin mRNAs that are highly expressed in most tumor tissues are selected as endogenous cancer indicators and therapy triggers to design the NC. Mice bearing breast cancer cells MCF-7 are prepared as a model to test its efficacy. The in vitro and in vivo assays validate that the NC show the capability for multiplexed mRNA imaging and high efficiency for logic-controlled combinational therapy of breast cancer.
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Affiliation(s)
- Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Tong Luo
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yao He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhiwei Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Hui Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jing Nie
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - De Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Shian Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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3
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He J, Nissim L, Soleimany AP, Binder-Nissim A, Fleming HE, Lu TK, Bhatia SN. Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection. ACS Synth Biol 2021; 10:2231-2242. [PMID: 34464083 DOI: 10.1021/acssynbio.1c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The integration of nanotechnology and synthetic biology could lay the framework for new classes of engineered biosensors that produce amplified readouts of disease states. As a proof-of-concept demonstration of this vision, here we present an engineered gene circuit that, in response to cancer-associated transcriptional deregulation, expresses heterologous enzyme biomarkers whose activity can be measured by nanoparticle sensors that generate amplified detection readouts. Specifically, we designed an AND-gate gene circuit that integrates the activity of two ovarian cancer-specific synthetic promoters to drive the expression of a heterologous protein output, secreted Tobacco Etch Virus (TEV) protease, exclusively from within tumor cells. Nanoparticle probes were engineered to carry a TEV-specific peptide substrate in order to measure the activity of the circuit-generated enzyme to yield amplified detection signals measurable in the urine or blood. We applied our integrated sense-and-respond system in a mouse model of disseminated ovarian cancer, where we demonstrated measurement of circuit-specific TEV protease activity both in vivo using exogenously administered nanoparticle sensors and ex vivo using quenched fluorescent probes. We envision that this work will lay the foundation for how synthetic biology and nanotechnology can be meaningfully integrated to achieve next-generation engineered biosensors.
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Affiliation(s)
- Jiang He
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lior Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ava P. Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft Research New England, Cambridge, Massachusetts 02142, United States
| | - Adina Binder-Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Family Medicine, Meuhedet Health Maintenance Organization, Tel Aviv 62038, Israel
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
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4
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Ausländer S, Ausländer D, Lang PF, Kemi M, Fussenegger M. Design of Multipartite Transcription Factors for Multiplexed Logic Genome Integration Control in Mammalian Cells. ACS Synth Biol 2020; 9:2964-2970. [PMID: 33213155 PMCID: PMC7684658 DOI: 10.1021/acssynbio.0c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Synthetic
biology relies on rapid and efficient methods to stably
integrate DNA payloads encoding for synthetic biological systems into
the genome of living cells. The size of designed biological systems
increases with their complexity, and novel methods are needed that
enable efficient and simultaneous integration of multiple payloads
into single cells. By assembling natural and synthetic protein–protein
dimerization domains, we have engineered a set of multipartite transcription
factors for driving heterologous target gene expression. With the
distribution of single parts of multipartite transcription factors
on piggyback transposon-based donor plasmids, we have created a logic
genome integration control (LOGIC) system that allows for efficient
one-step selection of stable mammalian cell lines with up to three
plasmids. LOGIC significantly enhances the efficiency of multiplexed
payload integration in mammalian cells compared to traditional cotransfection
and may advance cell line engineering in synthetic biology and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Paul F. Lang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Maarit Kemi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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5
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Macedo A, Gontijo AM. The intersectional genetics landscape for humans. Gigascience 2020; 9:giaa083. [PMID: 32761099 PMCID: PMC7407247 DOI: 10.1093/gigascience/giaa083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/05/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The human body is made up of hundreds-perhaps thousands-of cell types and states, most of which are currently inaccessible genetically. Intersectional genetic approaches can increase the number of genetically accessible cells, but the scope and safety of these approaches have not been systematically assessed. A typical intersectional method acts like an "AND" logic gate by converting the input of 2 or more active, yet unspecific, regulatory elements (REs) into a single cell type specific synthetic output. RESULTS Here, we systematically assessed the intersectional genetics landscape of the human genome using a subset of cells from a large RE usage atlas (Functional ANnoTation Of the Mammalian genome 5 consortium, FANTOM5) obtained by cap analysis of gene expression sequencing (CAGE-seq). We developed the heuristics and algorithms to retrieve and quality-rank "AND" gate intersections. Of the 154 primary cell types surveyed, >90% can be distinguished from each other with as few as 3 to 4 active REs, with quantifiable safety and robustness. We call these minimal intersections of active REs with cell-type diagnostic potential "versatile entry codes" (VEnCodes). Each of the 158 cancer cell types surveyed could also be distinguished from the healthy primary cell types with small VEnCodes, most of which were robust to intra- and interindividual variation. Methods for the cross-validation of CAGE-seq-derived VEnCodes and for the extraction of VEnCodes from pooled single-cell sequencing data are also presented. CONCLUSIONS Our work provides a systematic view of the intersectional genetics landscape in humans and demonstrates the potential of these approaches for future gene delivery technologies.
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Affiliation(s)
- Andre Macedo
- Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150–190, Lisbon, Portugal
| | - Alisson M Gontijo
- Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150–190, Lisbon, Portugal
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6
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Han X, Yang J, Zeng F, Weng J, Zhang Y, Peng Q, Shen L, Ding S, Liu K, Gao Y. Programmable Synthetic Protein Circuits for the Identification and Suppression of Hepatocellular Carcinoma. MOLECULAR THERAPY-ONCOLYTICS 2020; 17:70-82. [PMID: 32322664 PMCID: PMC7160531 DOI: 10.1016/j.omto.2020.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/02/2022]
Abstract
Precisely identifying and killing tumor cells are diligent pursuits in oncotherapy. Synthesized gene circuits have emerged as an intelligent weapon to solve these problems. Gene circuits based on post-transcriptional regulation enable a faster response than systems based on transcriptional regulation, which requires transcription and translation, showing superior safety. In this study, synthetic-promoter-free gene circuits possessing two control layers were constructed to improve the specific recognition of tumor cells. Using split-TEV, we designed and verified the basic control layer of protein-protein interaction (PPI) sensing. Another orthogonal control layer was built to sense specific proteins. Two layers were integrated to generate gene circuits sensing both PPI and specific proteins, forming 10 logic gates. To demonstrate the utility of this system, the circuit was engineered to sense alpha-fetoprotein (AFP) expression and the PPI between YAP and 14-3-3σ, the matching profile of hepatocellular carcinoma (HCC). Gene-circuit-loaded cells distinguished HCC from other cells and released therapeutic antibodies, exhibiting in vitro and in vivo therapeutic effects.
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Affiliation(s)
- Xu Han
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Fanhong Zeng
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jun Weng
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Yue Zhang
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Qing Peng
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Li Shen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Kaiyu Liu
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Yi Gao
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
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7
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Huang H, Liu Y, Liao W, Cao Y, Liu Q, Guo Y, Lu Y, Xie Z. Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy. Nat Commun 2019; 10:4801. [PMID: 31641136 PMCID: PMC6805884 DOI: 10.1038/s41467-019-12794-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/31/2019] [Indexed: 12/12/2022] Open
Abstract
Improving efficacy of oncolytic virotherapy remains challenging due to difficulty increasing specificity and immune responses against cancer and limited understanding of its population dynamics. Here, we construct programmable and modular synthetic gene circuits to control adenoviral replication and release of immune effectors selectively in hepatocellular carcinoma cells in response to multiple promoter and microRNA inputs. By performing mouse model experiments and computational simulations, we find that replicable adenovirus has a superior tumor-killing efficacy than non-replicable adenovirus. We observe a synergistic effect on promoting local lymphocyte cytotoxicity and systematic vaccination in immunocompetent mouse models by combining tumor lysis and secretion of immunomodulators. Furthermore, our computational simulations show that oncolytic virus which encodes immunomodulators can exert a more robust therapeutic efficacy than combinatorial treatment with oncolytic virus and immune effector. Our results provide an effective strategy to engineer oncolytic adenovirus, which may lead to innovative immunotherapies for a variety of cancers. It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of immunomodulators in hepatocellular carcinoma cells.
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Affiliation(s)
- Huiya Huang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Yiqi Liu
- Syngentech Inc., Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Weixi Liao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Yubing Cao
- Syngentech Inc., Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Qiang Liu
- Syngentech Inc., Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Yakun Guo
- Syngentech Inc., Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Yinying Lu
- The comprehensive Liver cancer center, The 5th medical center of PLA Genaral Hospital, 100 Xi-Si-Huan Middle Road, Beijing, 100039, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China.
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8
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Li S, Su W, Zhang C. Linear double‐stranded
DNA
s as innovative biological parts to implement genetic circuits in mammalian cells. FEBS J 2019; 286:2341-2354. [DOI: 10.1111/febs.14816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/11/2019] [Accepted: 03/21/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory Tianjin Medical University Cancer Institute and Hospital National Clinical Research Center for Cancer China
- Key Laboratory of Cancer Prevention and Therapy Tianjin China
- Tianjin's Clinical Research Center for Cancer China
| | - Weijun Su
- School of Medicine Nankai University Tianjin China
| | - Chunze Zhang
- Department of Colorectal Surgery Tianjin Union Medical Center China
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9
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Abstract
Noncoding RNAs (ncRNAs) play critical roles in essential cell fate decisions. However, the exact molecular mechanisms underlying ncRNA-mediated bistable switches remain elusive and controversial. In recent years, systematic mathematical and quantitative experimental analyses have made significant contributions on elucidating the molecular mechanisms of controlling ncRNA-mediated cell fate decision processes. In this chapter, we review and summarize the general framework of mathematical modeling of ncRNA in a pedagogical way and the application of this general framework on real biological processes. We discuss the emerging properties resulting from the reciprocal regulation between mRNA, miRNA, and competing endogenous mRNA (ceRNA), as well as the role of mathematical modeling of ncRNA in synthetic biology. Both the positive feedback loops between ncRNAs and transcription factors and the emerging properties from the miRNA-mRNA reciprocal regulation enable bistable switches to direct cell fate decision.
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10
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Quan K, Li J, Wang J, Xie N, Wei Q, Tang J, Yang X, Wang K, Huang J. Dual-microRNA-controlled double-amplified cascaded logic DNA circuits for accurate discrimination of cell subtypes. Chem Sci 2018; 10:1442-1449. [PMID: 30809361 PMCID: PMC6354832 DOI: 10.1039/c8sc04887h] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/17/2018] [Indexed: 12/14/2022] Open
Abstract
We have designed dual-microRNA-controlled cascaded logic DNA circuits for cancer cell subtype identification. The basic idea is to improve sensitivity by cascading DNAzyme and hybridization chain reaction (HCR), and improve accuracy by simultaneous detection of miR-122 and miR-21.
Accurate discrimination between different cells at the molecular level is particularly important for disease diagnosis. Endogenous RNAs are such molecular candidates for cancer cell subtype identification. But the key is that there is often low abundance of RNAs in live cells, or some RNAs are often shared by multiple types of cells. Thus, we have designed dual-microRNA-controlled double-amplified cascaded logic DNA circuits for cancer cell subtype identification. The basic idea is to improve sensitivity by cascading DNAzyme and hybridization chain reaction (HCR), and improve accuracy by simultaneous detection of miR-122 and miR-21. The in-tube and in-cell experimental results show that the cascaded logic DNA circuits can work and serve to differentiate the liver cancer cells Huh7 from other normal cells and cancer cells. We anticipate that this design can be widely applied in facilitating basic biomedical research and accurate disease diagnosis.
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Affiliation(s)
- Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Qiaomei Wei
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha , P. R. China .
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11
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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12
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Nissim L, Wu MR, Pery E, Binder-Nissim A, Suzuki HI, Stupp D, Wehrspaun C, Tabach Y, Sharp PA, Lu TK. Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy. Cell 2017; 171:1138-1150.e15. [PMID: 29056342 PMCID: PMC5986174 DOI: 10.1016/j.cell.2017.09.049] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/16/2017] [Accepted: 09/27/2017] [Indexed: 01/17/2023]
Abstract
Despite its success in several clinical trials, cancer immunotherapy remains limited by the rarity of targetable tumor-specific antigens, tumor-mediated immune suppression, and toxicity triggered by systemic delivery of potent immunomodulators. Here, we present a proof-of-concept immunomodulatory gene circuit platform that enables tumor-specific expression of immunostimulators, which could potentially overcome these limitations. Our design comprised de novo synthetic cancer-specific promoters and, to enhance specificity, an RNA-based AND gate that generates combinatorial immunomodulatory outputs only when both promoters are mutually active. These outputs included an immunogenic cell-surface protein, a cytokine, a chemokine, and a checkpoint inhibitor antibody. The circuits triggered selective T cell-mediated killing of cancer cells, but not of normal cells, in vitro. In in vivo efficacy assays, lentiviral circuit delivery mediated significant tumor reduction and prolonged mouse survival. Our design could be adapted to drive additional immunomodulators, sense other cancers, and potentially treat other diseases that require precise immunological programming.
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Affiliation(s)
- Lior Nissim
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ming-Ru Wu
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erez Pery
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adina Binder-Nissim
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroshi I Suzuki
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Doron Stupp
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, and Hadassah Medical School, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Claudia Wehrspaun
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, and Hadassah Medical School, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics , Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science , Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Biophysics Program, Harvard University, Boston, MA 02115, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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13
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Muldoon JJ, Donahue PS, Dolberg TB, Leonard JN. Building with intent: technologies and principles for engineering mammalian cell-based therapies to sense and respond. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017; 4:127-133. [PMID: 29450405 DOI: 10.1016/j.cobme.2017.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The engineering of cells as programmable devices has enabled therapeutic strategies that could not otherwise be achieved. Such strategies include recapitulating and enhancing native cellular functions and composing novel functions. These novel functions may be composed using both natural and engineered biological components, with the latter exemplified by the development of synthetic receptor and signal transduction systems. Recent advances in implementing these approaches include the treatment of cancer, where the most clinical progress has been made to date, and the treatment of diabetes. Principles for engineering cell-based therapies that are safe and effective are increasingly needed and beginning to emerge, and will be essential in the development of this new class of therapeutics.
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Affiliation(s)
- Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick S Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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Morel M. [Beating cancer with synthetic genes: towards more effective treatments through autonomous genetic programs]. Med Sci (Paris) 2017; 33:591-593. [PMID: 28990556 DOI: 10.1051/medsci/20173306011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Mathieu Morel
- Laboratoire PASTEUR, département de chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC-Université Paris 6, CNRS, 75005 Paris, France
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15
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Re A. Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology. Front Cell Dev Biol 2017; 5:77. [PMID: 28894736 PMCID: PMC5581392 DOI: 10.3389/fcell.2017.00077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/16/2017] [Indexed: 01/21/2023] Open
Abstract
Precision medicine in oncology needs to enhance its capabilities to match diagnostic and therapeutic technologies to individual patients. Synthetic biology streamlines the design and construction of functionalized devices through standardization and rational engineering of basic biological elements decoupled from their natural context. Remarkable improvements have opened the prospects for the availability of synthetic devices of enhanced mechanism clarity, robustness, sensitivity, as well as scalability and portability, which might bring new capabilities in precision cancer medicine implementations. In this review, we begin by presenting a brief overview of some of the major advances in the engineering of synthetic genetic circuits aimed to the control of gene expression and operating at the transcriptional, post-transcriptional/translational, and post-translational levels. We then focus on engineering synthetic circuits as an enabling methodology for the successful establishment of precision technologies in oncology. We describe significant advancements in our capabilities to tailor synthetic genetic circuits to specific applications in tumor diagnosis, tumor cell- and gene-based therapy, and drug delivery.
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Affiliation(s)
- Angela Re
- Centre for Sustainable Future Technologies, Istituto Italiano di TecnologiaTorino, Italy
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16
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Elitas M, Sadeghi S, Karamahmutoglu H, Gozuacik D, Serdar Turhal N. Microfabricated platforms to quantitatively investigate cellular behavior under the influence of chemical gradients. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa7400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Müller M, Ausländer S, Spinnler A, Ausländer D, Sikorski J, Folcher M, Fussenegger M. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat Chem Biol 2017; 13:309-316. [DOI: 10.1038/nchembio.2281] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023]
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18
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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