1.深圳大学医学部生物医学工程学院,广东省生物医学信息检测与超声成像重点实验室,广东 深圳 518060
2.深圳市第二人民医院,深圳市转化医学研究院,广东 深圳 518035
3.深圳市第二人民医院检验科,深圳市医学检验分子诊断重点实验室,广东 深圳 518035
4.深圳市第二人民医院神经外科,深圳市神经外科重点实验室,广东 深圳 518037
5.上海吐露港生物科技有限公司,上海 200233
[ "吕海龙(1988—),男,博士,博士后。研究方向为合成生物学及CRISPR分子诊断技术开发。E-mail: lvhailong8828@163.com" ]
[ "顾大勇(1972—),男,博士,主任技师,博士生导师、博士后合作导师。研究方向为生物芯片、生物传感技术。E-mail:wanhood@163.com" ]
收稿:2022-11-02,
修回:2022-12-17,
纸质出版:2023-04-30
移动端阅览
吕海龙, 王建, 吕浩, 王金, 徐勇, 顾大勇. 合成生物学在下一代基因诊断技术中的应用进展[J]. 合成生物学, 2023, 4(2): 318-332
LV Hailong, WANG Jian, LV Hao, WANG Jin, XU Yong, GU Dayong. Synthetic biology for next-generation genetic diagnostics[J]. Synthetic Biology Journal, 2023, 4(2): 318-332
吕海龙, 王建, 吕浩, 王金, 徐勇, 顾大勇. 合成生物学在下一代基因诊断技术中的应用进展[J]. 合成生物学, 2023, 4(2): 318-332 DOI: 10.12211/2096-8280.2022-061.
LV Hailong, WANG Jian, LV Hao, WANG Jin, XU Yong, GU Dayong. Synthetic biology for next-generation genetic diagnostics[J]. Synthetic Biology Journal, 2023, 4(2): 318-332 DOI: 10.12211/2096-8280.2022-061.
近年来,合成生物学技术取得了飞速的发展,与此同时也极大地推动了基因诊断领域的技术革新和应用拓展。准确诊断疾病和监测治疗后反应的检测方法对有效的临床管理至关重要,合成生物学作为一门以设计为导向的学科,试图重新设计生物系统,以便以可预测的方式执行新的功能,对这一领域的最新进展进行综述对疾病的预防、预测、诊断、治疗和预后具有重要意义。本文以该主题作为切入点,首先介绍了目前合成生物学在基因诊断中的应用类别,包括已经被开发出来的用于体外和体内的不同生物传感器;随后介绍了下一代基因诊断技术的发展方向以及基因诊断领域的合成生物学装置和技术进展;此外,本文讨论了目前基因诊断领域中存在的技术问题及其在临床应用中面临的挑战。最后,我们提请注意合成生物学中的最新创新,这些创新可能会对基因诊断的未来应用产生重大影响。
In recent years
rapid advances have been made for synthetic biology technologies
which contribute greatly to technological innovations and applications in genetic diagnostics. Diagnostic methods for accurate detection of diseases and monitoring treatment responses are essential for effective clinical managements. Synthetic biology seeks to redesign biological systems to perform new functions in a predictable manner. A review on recent advances in synthetic biology as a diagnostic method for accurate detection of diseases and monitoring therapeutic responses is essential for effective clinical management
and also important for prevention
prediction and prognosis of diseases. In this article
we first describes the categories of synthetic biology applications in genetic diagnostics
including different biosensors that have been developed for both
in vitro
and
in vivo
monitoring. Subsequently
perspectives of the next generation of genetic diagnostic technologies and progress of synthetic biology devices and technologies
in genetic diagnostics are highlighted. In addition
we further address the current technical challenges in genetic diagnostics and clinical applications. Finally
we draw attention to the latest innovations in synthetic biology that may have a significant impact on the future applications of genetic diagnostics.
TAN X , LETENDRE J H , COLLINS J J , et al . Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics [J ] . Cell , 2021 , 184 ( 4 ): 881 - 898 .
ZHOU T Y , LI R , ZHANG S T , et al . A copper-specific microbial fuel cell biosensor based on riboflavin biosynthesis of engineered Escherichia coli [J ] . Biotechnology and Bioengineering , 2021 , 118 ( 1 ): 210 - 222 .
HUI C Y , GUO Y , WU J , et al . Detection of bioavailable cadmium by double-color fluorescence based on a dual-sensing bioreporter system [J ] . Frontiers in Microbiology , 2021 , 12 : 696195 .
TRIVIÑO-VALENCIA J , LORA F , ZULUAGA J D , et al . Detection by PCR of pathogenic protozoa in raw and drinkable water samples in Colombia [J ] . Parasitology Research , 2016 , 115 ( 5 ): 1789 - 1797 .
PINTO-DUARTE V A , HÉRNANDEZ-ARANGO N M , MARIN-GALLEGO B J , et al . Detection of Giardia duodenalis and Toxoplasma gondii in soil and water samples in the Quindío River Basin, Colombia [J ] . Food and Waterborne Parasitology , 2022 , 28 : e00175 .
BAE K S , LEE S W , LEE J Y , et al . Development of diagnostic systems for wide range and highly sensitive detection of two waterborne hepatitis viruses from groundwater using the conventional reverse transcription nested PCR assay [J ] . Journal of Virological Methods , 2022 , 299 : 114344 .
JIA J , GUAN Y J , CHENG M Q , et al . Occurrence and distribution of antibiotics and antibiotic resistance genes in Ba River, China [J ] . Science of the Total Environment , 2018 , 642 : 1136 - 1144 .
AHMED W , GYAWALI P , HAMILTON K A , et al . Antibiotic resistance and sewage-associated marker genes in untreated sewage and a river characterized during baseflow and stormflow [J ] . Frontiers in Microbiology , 2021 , 12 : 632850 .
CHEN X J , WANG B J , THOMPSON I P , et al . Rational design and characterization of nitric oxide biosensors in E. coli Nissle 1917 and mini SimCells [J ] . ACS Synthetic Biology , 2021 , 10 ( 10 ): 2566 - 2578 .
TAKAHASHI M K , TAN X , DY A J , et al . A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers [J ] . Nature Communications , 2018 , 9 : 3347 .
TAKAHASHI M K , TAN X , DY A J . Cell-free paper-based analysis of gut microbiota and host biomarkers [J ] . Methods in Molecular Biology , 2022 , 2433 : 351 - 374 .
MAO N , CUBILLOS-RUIZ A , CAMERON D E , et al . Probiotic strains detect and suppress cholera in mice [J ] . Science Translational Medicine , 2018 , 10 ( 445 ): eaao2586 .
SCHOOF M , FAUST B , SAUNDERS R A , et al . An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike [J ] . Science , 2020 , 370 ( 6523 ): 1473 - 1479 .
RICHNER J M , HIMANSU S , DOWD K A , et al . Modified mRNA vaccines protect against Zika virus infection [J ] . Cell , 2017 , 168 ( 6 ): 1114 - 1125.e10 .
MEESING A , RAZONABLE R R . New developments in the management of cytomegalovirus infection after transplantation [J ] . Drugs , 2018 , 78 ( 11 ): 1085 - 1103 .
TUCCI F , SCARAMUZZA S , AIUTI A , et al . Update on clinical ex vivo hematopoietic stem cell gene therapy for inherited monogenic disea ses [J ] . Molecular Therapy , 2021 , 29 ( 2 ): 489 - 504 .
CHENG R H , LIANG J Y , LI Y , et al . Next-generation sequencing through multi-gene panel testing for diagnosis of hereditary ichthyosis in Chinese [J ] . Clinical Genetics , 2020 , 97 ( 5 ): 770 - 778 .
WU M R , JUSIAK B , LU T K . Engineering advanced cancer therapies with synthetic biology [J ] . Nature Reviews Cancer , 2019 , 19 ( 4 ): 187 - 195 .
SHIMABUKURO-VORNHAGEN A , BÖLL B , SCHELLONGOWSKI P , et al . Critical care management of chimeric antigen receptor T-cell therapy recipients [J ] . CA : a Cancer Journal for Clinicians , 2022 , 72 ( 1 ): 78 - 93 .
DIMITRI A , HERBST F , FRAIETTA J A . Engineering the next-generation of CAR T-cells with CRISPR-Cas9 gene editing [J ] . Molecular Cancer , 2022 , 21 ( 1 ): 78 .
HONG F , MA D , WU K Y , et al . Precise and programmable detection of mutations using ultraspecific riboregulators [J ] . Cell , 2020 , 180 ( 5 ): 1018 - 1032.e16 .
RYLOTT E L , BRUCE N C . How synthetic biology can help bioremediation [J ] . Current Opinion in Chemical Biology , 2020 , 58 : 86 - 95 .
PARUCH L . Molecular diagnostic tools applied for assessing microbial water quality [J ] . International Journal of Environmental Research and Public Health , 2022 , 19 ( 9 ): 5128 .
YAASHIKAA P R , DEVI M K , KUMAR P S . Engineering microbes for enhancing the degradation of environmental pollutants: a detailed review on synthetic biology [J ] . Environmental Research , 2022 , 214 ( Pt 1 ): 113868 .
THAVARAJAH W , VEROSLOFF M S , JUNG J K , et al . A primer on emerging field-deployable synthetic biology tools for global water quality monitoring [J ] . Npj Clean Water , 2020 , 3 : 18 .
DOU J , BENNETT M R . Synthetic biology and the gut microbiome [J ] . Biotechnology Journal , 2018 , 13 ( 5 ): 1700159 .
RAMACHANDRAN G , BIKARD D . Editing the microbiome the CRISPR way [J ] . Philosophical Transactions of the Royal Society B: Biological Sciences , 2019 , 374 ( 1772 ): 20180103 .
MIMEE M , TUCKER A C , VOIGT C A , et al . Programming a human commensal bacterium, Bacteroides thetaiotaomicron , to sense and respond to stimuli in the murine gut microbiota [J ] . Cell Systems , 2015 , 1 ( 1 ): 62 - 71 .
SINGH R P , SHADAN A , MA Y . Biotechnological applications of probiotics: a multifarious weapon to disease and metabolic abnormality [J ] . Probiotics and Antimicrobial Proteins , 2022 , 14 ( 6 ): 1184 - 1210 .
MILLS H , ACQUAH R , TANG N , et al . The use of bacteria in cancer treatment: a review from the perspective of cellular microbiology [J ] . Emergency Medicine International , 2022 , 2022 : 8127137 .
CRESCI G A M , LAMPE J W , GIBSON G . Targeted approaches for in situ gut microbiome manipulation [J ] . JPEN Journal of Parenteral and Enteral Nutrition , 2020 , 44 ( 4 ): 581 - 588 .
BOBER J R , BEISEL C L , NAIR N U . Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications [J ] . Annual Review of Biomedical Engineering , 2018 , 20 : 277 - 300 .
CAÑEZ C , SELLE K , GOH Y J , et al . Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus [J ] . FEMS Microbiology Letters , 2019 , 366 ( 9 ): fnz105 .
KUMAR P , SINHA R , SHUKLA P . Artificial intelligence and synthetic biology approaches for human gut microbiome [J ] . Critical Reviews in Food Science and Nutrition , 2022 , 62 ( 8 ): 2103 - 2121 .
VOORHEES P J , CRUZ-TERAN C , EDELSTEIN J , et al . Challenges & opportunities for phage-based in situ microbiome engineering in the gut [J ] . Journal of Controlled Release , 2020 , 326 : 106 - 119 .
BARANI M , RAHDAR A , SARGAZI S , et al . Nanotechnology for inflammatory bowel disease management: detection, imaging and treatment [J ] . Sensing and Bio-Sensing Research , 2021 , 32 : 100417 .
NJUE F , CHIH S . When to intervene for donor-specific antibody after heart transplantation [J ] . Current Opinion in Organ Transplantation , 2019 , 24 ( 3 ): 271 - 278 .
SU J A , BAXTER-LOWE L A , KANTOR P F , et al . The clinical impact of donor-specific antibodies on antibody-mediated rejection and long-term prognosis after heart transplantation [J ] . Current Opinion in Organ Transplantation , 2019 , 24 ( 3 ): 245 - 251 .
ROTH T L , MARSON A . Genetic disease and therapy [J ] . Annual Review of Pathology , 2021 , 16 : 145 - 166 .
BHARATHKUMAR N , SUNIL A , MEERA P , et al . CRISPR/Cas-based modifications for therapeutic applications: a review [J ] . Molecular Biotechnology , 2022 , 64 ( 4 ): 355 - 372 .
LIN H F , LI G , PENG X W , et al . The use of CRISPR/Cas9 as a tool to study human infectious viruses [J ] . Frontiers in Cellular and Infection Microbiology , 2021 , 11 : 590989 .
SHARMA G , SHARMA A R , BHATTACHARYA M , et al . CRISPR-Cas9: a preclinical and clinical perspective for the treatment of human diseases [J ] . Molecular Therapy , 2021 , 29 ( 2 ): 571 - 586 .
KANG K , SONG Y , KIM I , et al . Therapeutic applications of the CRISPR-Cas system [J ] . Bioengineering , 2022 , 9 ( 9 ): 477 .
PICKAR-OLIVER A , GERSBACH C A . The next generation of CRISPR-Cas technologies and applications [J ] . Nature Reviews Molecular Cell Biology , 2019 , 20 ( 8 ): 490 - 507 .
WANG X S , XIONG E H , TIAN T , et al . Clustered regularly interspaced short palindromic repeats/Cas9-mediated lateral flow nucleic acid assay [J ] . ACS Nano , 2020 , 14 ( 2 ): 2497 - 2508 .
KLEINSTIVER B P , SOUSA A A , WALTON R T , et al . Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing [J ] . Nature Biotechnology , 2019 , 37 ( 3 ): 276 - 282 .
CHEN J S , MA E B , HARRINGTON L B , et al . CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity [J ] . Science , 2018 , 360 ( 6387 ): 436 - 439 .
LI S Y , CHENG Q X , WANG J M , et al . CRISPR-Cas12a-assisted nucleic acid detection [J ] . Cell Discovery , 2018 , 4 : 20 .
LV H L , WANG J , ZHANG J , et al . Definition of CRISPR Cas12a trans-cleavage units to facilitate CRISPR diagnostics [J ] . Frontiers in Microbiology , 2021 , 12 : 766464 .
LI Y , LI S Y , WANG J , et al . CRISPR/Cas systems towards next-generation biosensing [J ] . Trends in Biotechnology , 2019 , 37 ( 7 ): 730 - 743 .
KHAN A , OSTAKU J , ARAS E , et al . Combating infectious diseases with synthetic biology [J ] . ACS Synthetic Biology , 2022 , 11 ( 2 ): 528 - 537 .
HUANG Z , TIAN D , LIU Y , et al . Ultra-sensitive and high-throughput CRISPR-powered COVID-19 diagnosis [J ] . Biosensors & Bioelectronics , 2020 , 164 : 112316 .
BROTO M , KAMINSKI M M , ADRIANUS C , et al . Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs [J ] . Nature Nanotechnology , 2022 , 17 ( 10 ): 1120 - 1126 .
ZOU Y P , MASON M G , BOTELLA J R . Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics [J ] . PLoS One , 2020 , 15 ( 6 ): e0235216 .
MUSTAFA M I , MAKHAWI A M . SHERLOCK and DETECTR: CRISPR-Cas systems as potential rapid diagnostic tools for emerging infectious diseases [J ] . Journal of Clinical Microbiology , 2021 , 59 ( 3 ): e00745 - e00720 .
LEE R A , PUIG H , NGUYEN P Q , et al . Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2020 , 117 ( 41 ): 25722 - 25731 .
MANGHWAR H , LINDSEY K , ZHANG X L , et al . CRISPR/Cas system: recent advances and future prospects for genome editing [J ] . Trends in Plant Science , 2019 , 24 ( 12 ): 1102 - 1125 .
KIM J , CAMPBELL A S , DE ÁVILA B E F , et al . Wearable biosensors for healthcare monitoring [J ] . Nature Biotechnology , 2019 , 37 ( 4 ): 389 - 406 .
NGUYEN P Q , SOENKSEN L R , DONGHIA N M , et al . Wearable materials with embedded synthetic biology sensors for biomolecule detection [J ] . Nature Biotechnology , 2021 , 39 ( 11 ): 1366 - 1374 .
RHEA K A , MCDONALD N D , COLE S D , et al . Variability in cell-free expression reactions can impact qualitative genetic circuit characterization [J ] . Synthetic Biology , 2022 , 7 ( 1 ): ysac011 .
SADAT MOUSAVI P , SMITH S J , CHEN J B , et al . A multiplexed, electrochemical interface for gene-circuit-based sensors [J ] . Nature Chemistry , 2020 , 12 ( 1 ): 48 - 55 .
LAI W , XIONG X W , WANG F , et al . Nonlinear regulation of enzyme-free DNA circuitry with ultrasensitive switches [J ] . ACS Synthetic Biology , 2019 , 8 ( 9 ): 2106 - 2112 .
KIM H , SKINNER D J , GLASS D S , et al . 4-Bit adhesion logic enables universal multicellular interface patterning [J ] . Nature , 2022 , 608 ( 7922 ): 324 - 329 .
NAJJAR D , RAINBOW J , SHARMA TIMILSINA S , et al . A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma [J ] . Nature Biomedical Engineering , 2022 , 6 ( 8 ): 968 - 978 .
BHADRA S , POTHUKUCHY A , SHROFF R , et al . Cellular reagents for diagnostics and synthetic biology [J ] . PLoS One , 2018 , 13 ( 8 ): e0201681 .
SHAO Y Y , LU N , WU Z F , et al . Creating a functional single-chromosome yeast [J ] . Nature , 2018 , 560 ( 7718 ): 331 - 335 .
OOIJEVAAR R E , TERVEER E M , VERSPAGET H W , et al . Clinical application and potential of fecal microbiota transplantation [J ] . Annual Review of Medicine , 2019 , 70 : 335 - 351 .
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