When synthetic biology meets medicine

Abstract

In recent years, the world has faced significant challenges with the coronavirus disease 2019 (COVID-19) pandemic, as well as other infectious diseases such as Zika and Ebola. Furthermore, the rapid rise of non-communicable diseases such as diabetes, heart disease, and cancer has placed tremendous strain on healthcare resources and systems. Unfortunately, advancements in drug development, diagnostics, and therapeutics have struggled to keep pace with the emergence and progression of diseases, necessitating the exploration of new technologies for the discovery and development of biomedicines and biotherapies. Synthetic biology, a revolutionary field in modern science, holds great promise in advancing drug development and disease treatment. This review provides a comprehensive overview of recent developments in the application of synthetic biology to medicine, with a specific focus on its role in drug discovery, drug production, and the diagnosis and treatment of various diseases.

Keywords

synthetic biology / medicine / disease diagnosis / disease treatment / metabolic engineering

References

[1] Zheng T, Zhang M, Wu L, et al. Upcycling CO₂ into energy-rich long-chain compounds via electrochemical and metabolic engineering. Nat Catal 2022;5:388–96.

[2] Tao C, Hongbing S, Yanhe M et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 2021;373:1523–7.

[3] Yan X, Liu X, Zhao C, et al. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023;8:199.

[4] Tan X, Letendre JH, Collins JJ, et al. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021;184:881–98.

[5] Baltz RH. Streptomyces and saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 2010;37:759–72.

[6] Komatsu M, Uchiyama T, Omura S, et al. Genome-minimized streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci U S A 2010;107:2646–51.

[7] Ma Z, Wang PG. RecET direct cloning of polysaccharide gene cluster from gram-negative bacteria. Methods Mol Biol 2019;1954:15–23.

[8] Liu J, Wang X, Dai G, et al. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022;59:107966.

[9] Chae TU, Choi SY, Kim JW, et al. Recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol 2017;47:67–82.

[10] Lee N, Hwang S, Lee Y, et al. Synthetic biology tools for novel secondary metabolite discovery in Streptomyces. J Microbiol Biotechnol 2019;29:667–86.

[11] Zhang LY, Chang SH, Wang J. How to make a minimal genome for synthetic minimal cell. Protein Cell. 2010;1:427–34.

[12] Ke J, Yoshikuni Y. Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 2020;62:88–97.

[13] Polka JK, Silver PA. Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression. PeerJ 2014;2:e597.

[14] Palazzotto E, Tong Y, Lee SY, et al. Synthetic biology and metabolic engineering of actinomycetes for natural product discovery. Biotechnol Adv 2019;37:107366.

[15] Dai J, Boeke JD, Luo Z, et al. Sc3.0: revamping and minimizing the yeast genome. Genome Biol 2020;21:205.

[16] de la Torre D, Chin JW. Reprogramming the genetic code. Nat Rev Genet 2021;22:169–84.

[17] Farhi M, Marhevka E, Ben-Ari J, et al. Generation of the potent anti- malarial drug artemisinin in tobacco. Nat Biotechnol 2011;29:1072–4.

[18] Reed J, Osbourn A. Engineering terpenoid production through transient expression in Nicotiana benthamiana. Plant Cell Rep 2018;37:1431–41.

[19] Cravens A, Payne J, Smolke CD. Synthetic biology strategies for microbial biosynthesis of plant natural products. Nat Commun 2019;10:2142.

[20] Yang D, Park SY, Park YS, et al. Metabolic engineering of Escherichia coli for natural product biosynthesis. Trends Biotechnol 2020;38:745–65.

[21] Polakowski T, Stahl U, Lang C. Overexpression of a cytosolic hydroxymethylglutaryl-CoA reductase leads to squalene accumulation in yeast. Appl Microbiol Biotechnol 1998;49:66–71.

[22] Li R, Wang K, Wang D, et al. Production of plant volatile terpenoids (rose oil) by yeast cell factories. Green Chem 2021;23:5088–96.

[23] Fang Z, Jones JA, Koffas MAG et al. Engineering Escherichia coli Co-cultures for production of curcuminoids from glucose. Biotechnol J 2018;13:e1700576.

[24] Galanie S, Thodey K, Smolke CD, et al. Complete biosynthesis of opioids in yeast. Science 2015;349:1095–100.

[25] Li X, Yan Y, Xia H, et al. Enhancement of milbemycins production by phosphopantetheinyl transferase and regulatory pathway engineering in Streptomyces bingchenggensis. World J Microbiol Biotechnol 2023;39:278.

[26] Yan YS, Xia HY. Recent advances in the research of milbemycin biosynthesis and regulation as well as strategies for strain improvement. Arch Microbiol 2021;203:5849–57.

[27] Kim MS, Cho WJ, Yoon YJ, et al. Engineered biosynthesis of milbemycins in the avermectin high-producing strain Streptomyces avermitilis. Microb Cell Fact 2017;16:9.

[28] Liu Q, Shen Q, Zhang Y, et al. Simple and rapid direct cloning and heterologous expression of natural product biosynthetic gene cluster in Bacillus subtilis via Red/ET recombineering. Sci Rep 2016;6:34623.

[29] Demain AL. Pharmaceutically active secondary metabolites of microorganisms. Appl Microbiol Biotechnol 1999;52:455–63.

[30] Nielsen J, Keasling JD. Engineering cellular metabolism. Cell 2016;164:1185–97.

[31] Paddon CJ, Keasling JD. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014;12:355–67.

[32] Camacho-Zaragoza JM, Hernández-Chávez G, Gosset G, et al. Engineering of a microbial coculture of Escherichia coli strains for the biosynthesis of resveratrol. Microb Cell Fact 2016;15:163.

[33] Jones JA, Vernacchio VR, Collins SM, et al. Complete biosynthesis of anthocyanins using E. coli polycultures. mBio 2017;8:e00621–17.

[34] Tsuruta H, Paddon CJ, Keasling JD, et al. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 2009;4:e4489.

[35] Paddon CJ, Keasling JD, Newman JD, et al. High-level semi- synthetic production of the potent antimalarial artemisinin. Nature 2013;496:528–32.

[36] Huang Q, Roessner CA, Scott AI, et al. Engineering Escherichia coli for the synthesis of taxadiene, a key intermediate in the biosynthesis of taxol. Bioorg Med Chem 2001;9:2237–42.

[37] Engels B, Dahm P, Jennewein S. Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metab Eng 2008;10:201–6.

[38] Wu P, Wan D, Xu G, et al. An unusual protector-protégé strategy for the biosynthesis of purine nucleoside antibiotics. Cell Chem Biol 2017;24:171–81.

[39] Tanino T, Aoki T, Chung WY, et al. Improvement of a Candida antarctica lipase B-displaying yeast whole-cell biocatalyst and its application to the polyester synthesis reaction. Appl Microbiol Biotechnol 2009;82:59–66.

[40] Angov E, Hillier CJ, Kincaid RL, et al. Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One 2008;3:e2189.

[41] Zawada JF, Burgenson D, Kiss RD, et al. Cell-free technologies for biopharmaceutical research and production. Curr Opin Biotechnol 2022;76:102719.

[42] Zawada JF, Yin G, Steiner AR, et al. Microscale to manufacturing scale-up of cell-free cytokine production—a new approach for short-ening protein production development timelines. Biotechnol Bioeng 2011;108:1570–8.

[43] Yin G, Stephenson HT, Yang J, et al. RF1 attenuation enables efficient non-natural amino acid incorporation for production of homogeneous antibody drug conjugates. Sci Rep 2017;7:3026.

[44] Groff D, Armstrong S, Rivers PJ, et al. Engineering toward a bacterial “endoplasmic reticulum” for the rapid expression of immunoglobulin proteins. MAbs 2014;6:671–8.

[45] Yin G, Garces ED, Yang J, et al. Aglycosylated antibodies and antibody fragments produced in a scalable in vitro transcription- translation system. MAbs 2012;4:217–25.

[46] Korman TP, Opgenorth PH, Bowie JU. A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nat Commun 2017;8:15526.

[47] Dudley QM, Nash CJ, Jewett MC. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol 2019;4:ysz003.

[48] Grubbe WS, Rasor BJ, Krüger A, et al. Cell-free styrene biosynthesis at high titers. Metab Eng 2020;61:89–95.

[49] Georgi V, Georgi L, Blechert M, et al. On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode. Lab Chip 2016;16:269–81.

[50] Martin RW, Majewska NI, Chen CX, et al. Development of a CHO-based cell-free platform for synthesis of active monoclonal antibodies. ACS Synth Biol 2017;6:1370–9.

[51] Hershewe JM, Warfel KF, Iyer SM, et al. Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles. Nat Commun 2021;12:2363.

[52] Dondapati SK, Stech M, Zemella A, et al. Cell-free protein synthesis: a promising option for future drug development. BioDrugs. 2020;34:327–48.

[53] Chen J, Fan F, Qu G, et al. Identification of Absidia orchidis steroid 11β-hydroxylation system and its application in engineering Saccharomyces cerevisiae for one-step biotransformation to produce hydrocortisone. Metab Eng 2020;57:31–42.

[54] Ibrahim GG, Yan J, Xu L, et al. Resveratrol production in yeast hosts: current status and perspectives. Biomolecules 2021;11:830.

[55] Li M, Kildegaard KR, Chen Y, et al. De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. Metab Eng 2015;32:1–11.

[56] Qiaorui J, Danyang S, Haibei L, et al. Synthesis of 5- hydroxytryptophan by recombinant Escherichia coli expressing Bacillus SP phenylalanine hydroxylase. YINGYANGXUEBAO. 2021;43:294–97 (in Chinese).

[57] Elander RP. Industrial production of beta-lactam antibiotics. Appl Microbiol Biotechnol 2003;61:385–92.

[58] Stassi D, Donadio S, Staver MJ, et al. Identification of a Saccharopolyspora erythraea gene required for the final hydroxylation step in erythromycin biosynthesis. J Bacteriol 1993;175:182–9.

[59] Ford LM, Eaton TE, Godfrey OW. Selection of Streptomyces ambofaciens mutants that produce large quantities of spiramycin and determination of optimal conditions for spiramycin production. Appl Environ Microbiol 1990;56:3511–4.

[60] Lawen A. Biosynthesis of cyclosporins and other natural peptidyl prolyl cis/trans isomerase inhibitors. Biochim Biophys Acta 2015;1850:2111–20.

[61] Cruz MC, Cavallo LM, Görlach JM, et al. Rapamycin antifungal action is mediated via conserved complexes with FKBP12 and TOR kinase homologs in Cryptococcus neoformans. Mol Cell Biol 1999;19:4101–12.

[62] Xu W, Chooi YH, Choi JW, et al. the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew Chem Int Ed Engl 2013;52:6472–5.

[63] Ajikumar PK, Xiao WH, Tyo KEJ, et al. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 2010;330:70–4.

[64] Gemperlein K, Dietrich D, Kohlstedt M, et al. Polyunsaturated fatty acid production by Yarrowia lipolytica employing designed myxobacterial PUFA synthases. Nat Commun 2019;10:4055.

[65] Lau W, Sattely ES. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science 2015;349:1224–8.

[66] Luo XZ, Reiter MA, D’espaux L, et al. Complete bio-synthesis of cannabinoids and their unnatural analogues in yeast. Nature 2019;567:123–6.

[67] Li J, Zhang X, Renata H. Asymmetric chemoenzymatic synthesis of ((-))-podophyllotoxin and related aryltetralin lignans. Angew Chem Int Ed 2019;58:11657–60.

[68] Yoneji T, Fujita H, Mukai T, et al. Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes. Nucleic Acids Res 2021;49:8407–18.

[69] Gibson DG, Benders GA, Smith HO, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008;319:1215–20.

[70] Richardson SM, Mitchell LA, Stracquadanio G, et al. Design of a synthetic yeast genome. Science 2017;355:1040–4.

[71] Zhu HQ, Tang XL, Zheng RC, et al. Recent advancements in enzyme engineering via site-specific incorporation of unnatural amino acids. World J Microbiol Biotechnol 2021;37:213.

[72] Smolskaya S, Andreev YA. Site-specific incorporation of unnatural amino acids into Escherichia coli recombinant protein: methodology development and recent achievement. Biomolecules 2019;9:255.

[73] Bedard PL, Hyman DM, Davids MS, et al. Small molecules, big impact: 20 years of targeted therapy in oncology. Lancet 2020;395:1078–88.

[74] Wang N, Wang L. Genetically encoding latent bioreactive amino acids and the development of covalent protein drugs. Curr Opin Chem Biol 2022;66:102106.

[75] Xu XX, Zhu J, Huang DZ, et al. Total synthesis of arteannuin and deoxyarteannuin. Tetrahedron 1986;42:819–28.

[76] Dai ZB, Liu Y, Zhang XN, et al. Metabolic engineering of Saccharomyces cerevisiae for production of ginsenosides. Metab Eng 2013;20:146–56.

[77] Dai ZB, Wang BB, Liu Y, et al. Producing aglycons of ginsenosides in bakers’ yeast. Sci Rep 2014;4:3698.

[78] Wang PP, Wei W, Ye W, et al. Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at high-efficiency. Cell Discovery 2019;5:5.

[79] Benamu E, Gajurel K, Deresinski S, et al. Plasma microbial cell-free DNA next-generation sequencing in the diagnosis and management of febrile neutropenia. Clin Infect Dis 2022;74:1659–68.

[80] Yan L, Sun W, Lu Z, et al. Metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of Tuberculosis meningitis in HIV-negative population. Int J Infect Dis 2020;96: 270–5.

[81] Li N, Cai Q, Hu B, et al. High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods 2021;5:2000792.

[82] Hoffmann B, Tappe D, Beer M, et al. A variegated squirrel bornavirus associated with fatal human encephalitis. N Engl J Med 2015;373:154–62.

[83] Ai JW, Weng SS, Zhang WH, et al. Human endophthalmitis caused by pseudorabies virus infection, China, 2017. Emerg Infect Dis 2018;24:1087–90.

[84] Sanger F, Air GM, Barrell BG, et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977;265:687–95.

[85] Anderson S, Bankier AT, Barrell BG, et al. Sequence and organization of the human mitochondrial genome. Nature 1981;290:457–65.

[86] Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496–512.

[87] Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science 1996;274:546, 563–7.

[88] Claussnitzer M, Cho JH, Collins R, et al. A brief history of human disease genetics. Nature 2020;577:179–89.

[89] Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008;9:387–402.

[90] Huang X, Han B. Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol 2014;65:531–51.

[91] Plassais J, Kim J, Davis BW, et al. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nat Commun 2019;10:1489.

[92] Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet 2019;20:341–55.

[93] Varshney RK, Nayak SN, May GD, et al. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 2009;27:522–30.

[94] Wu J, Wu M, Chen T, et al. Whole genome sequencing and its applications in medical genetics. Quant Biol 2016;4:115–28.

[95] Quick J, Grubaugh ND, Pullan ST, et al. Multiplex PCR method for MinION and illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12:1261–76.

[96] Vollger MR, Guitart X, Dishuck PC, et al. Segmental duplications and their variation in a complete human genome. Science 2022;376:eabj6965.

[97] Nurk S, Koren S, Rhie A et al. The complete sequence of a human genome. Science 2022;376:44–53.

[98] Hoyt SJ, Storer JM, Hartley GA, et al. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 2022;376:eabk3112.

[99] Gershman A, Sauria MEG, Guitart X, et al. Epigenetic patterns in a complete human genome. Science 2022;376:eabj5089.

[100] Altemose N, Logsdon GA, Bzikadze AV, et al. Complete genomic and epigenetic maps of human centromeres. Science 2022;376:eabl4178.

[101] English MA, Gayet RV, Collins JJ. Designing biological circuits: synthetic biology within the operon model and beyond. Annu Rev Biochem 2021;90:221–44.

[102] Barger N, Oren I, Li X, et al. A whole-cell bacterial biosensor for blood markers detection in urine. ACS Synth Biol 2021;10:1132–42.

[103] Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020;38:870–4.

[104] Ding N, Zhou S, Deng Y. Transcription-factor-based biosensor engineering for applications in synthetic biology. ACS Synth Biol 2021;10:911–22.

[105] Green AA, Silver PA, Collins JJ, et al. Toehold switches: de-novo-designed regulators of gene expression. Cell 2014;159:925–39.

[106] He MY, Lin YJ, Kao YL, et al. Sensitive and specific cadmium biosensor developed by reconfiguring metal transport and leveraging natural gene repositories. ACS Sens 2021;6:995–1002.

[107] Jha RK, Kern TL, Kim Y, et al. A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor. Nucleic Acids Res 2016;44:8490–500.

[108] Zhou T, Li R, Zhang S, et al. A copper-specific microbial fuel cell biosensor based on riboflavin biosynthesis of engineered Escherichia coli. Biotechnol Bioeng 2021;118:210–22.

[109] Wan X, Volpetti F, Petrova E, et al. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat Chem Biol 2019;15:540–8.

[110] Luisi B, Hegab R, Person C, et al. Engineered biosensors in an encapsulated and deployable system for environmental chemical detection. ACS Sens 2022;7:2589–96.

[111] Woo SG, Moon SJ, Kim SK, et al. A designed whole-cell biosensor for live diagnosis of gut inflammation through nitrate sensing. Biosens Bioelectron 2020;168:112523.

[112] Lopreside A, Wan X, Michelini E, et al. Comprehensive profiling of diverse genetic reporters with application to whole-cell and cell-free biosensors. Anal Chem 2019;91:15284–92.

[113] Moraskie M, Roshid MHO, O’Connor G, et al. Microbial whole-cell biosensors: current applications, challenges, and future perspectives. Biosens Bioelectron 2021;191:113359.

[114] Nguyen PQ, Soenksen LR, Donghia NM, et al. Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nat Biotechnol 2021;39:1366–74.

[115] Pardee K, Green AA, Takahashi MK, et al. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 2016;165:1255–66.

[116] Zhang Y, Zhao C, Bi H, et al. A cell-free paper-based biosensor dependent on allosteric transcription factors (aTFs) for on-site detection of harmful metals Hg²⁺ and Pb²⁺ in water. J Hazard Mater 2022;438:129499.

[117] Jung JK, Alam KK, Verosloff MS, et al. Cell-free biosensors for rapid detection of water contaminants. Nat Biotechnol 2020;38: 1451–9.

[118] Tang Y, Song T, Gao L, et al. A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples. Nat Commun 2022;13:4667.

[119] Karlikow M, da Silva SJR, Guo Y, et al. Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples. Nat Biomed Eng 2022;6: 246–56.

[120] Zhou W, Hu L, Ying L, et al. A CRISPR-Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 2018;9:5012.

[121] Shen J, Zhou X, Shan Y, et al. Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun 2020;11:267.

[122] Zhang L, Guo W, Lu Y. Advances in cell-free biosensors: principle, mechanism, and applications. Biotechnol J 2020;15:e2000187.

[123] Zhang Y, Zou ZP, Chen SY, et al. Design and optimization of E. coli artificial genetic circuits for detection of explosive composition 2,4-dinitrotoluene. Biosens Bioelectron 2022;207:114205.

[124] Landrum MJ, Lee JM, Benson M, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 2016;44:D862–8.

[125] Yanpanitch OU, Hatairaktham S, Charoensakdi R, et al. Treatment of β-thalassemia/hemoglobin E with antioxidant cocktails results in decreased oxidative stress, increased hemoglobin concentration, and improvement of the hypercoagulable state. Oxid Med Cell Longev 2015;2015:537954.

[126] Grasemann H, Stehling F, Brunar H, et al. Inhalation of Moli1901 in patients with cystic fibrosis. Chest 2007;131:1461–6.

[127] Devine MJ, Ryten M, Vodicka P, et al. Parkinson’s disease induced pluripotent stem cells with triplication of the α-synuclein locus. Nat Commun 2011;2:440.

[128] Drouet V, Ruiz M, Zala D, et al. Allele-specific silencing of mutant huntingtin in rodent brain and human stem cells. PLoS One 2014;9:e99341.

[129] Rando TA. The dystrophin-glycoprotein complex, cellular signaling, and the regulation of cell survival in the muscular dystrophies. Muscle Nerve 2001;24:1575–94.

[130] Bonomo ME, Deem MW. The physicist’s guide to one of biotechnology’s hottest new topics: CRISPR-Cas. Phys Biol 2018;15:041002.

[131] Rafeeq MM, Murad HAS. Cystic fibrosis: current therapeutic targets and future approaches. J Transl Med 2017;15:84.

[132] Arias-Fuenzalida J, Jarazo J, Qing X, et al. FACS-assisted CRISPR-Cas9 genome editing facilitates Parkinson’s disease modeling. Stem Cell Rep 2017;9:1423–31.

[133] Yang S, Chang R, Yang H, et al. CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington’s disease. J Clin Invest 2017;127:2719–24.

[134] Aartsma-Rus A, Krieg AM. FDA approves Eteplirsen for Duchenne muscular dystrophy: the next chapter in the Eteplirsen saga. Nucleic Acid Ther 2017;27:1–3.

[135] Weatherall DJ, Clegg JB. Thalassemia—a global public health problem. Nat Med 1996;2:847–9.

[136] Dever DP, Bak RO, Porteus MH, et al. CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells. Nature 2016;539:384–9.

[137] Krokan HE, Bjørås M. Base excision repair. Cold Spring Harb Perspect Biol 2013;5:a012583.

[138] Anzalone AV, Randolph PB, Liu DR, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 2019;576:149–57.

[139] Nowak KJ, Davies KE. Duchenne muscular dystrophy and dystrophin: pathogenesis and opportunities for treatment. EMBO Rep 2004;5:872–6.

[140] Chemello F, Chai AC, Li H, et al. Precise correction of Duchenne muscular dystrophy exon deletion mutations by base and prime editing. Sci Adv 2021;7:eabg4910.

[141] Geurts MH, de Poel E, Amatngalim GD, et al. CRISPR-based adenine editors correct nonsense mutations in a cystic fibrosis organoid biobank. Cell Stem Cell 2020;26:503–510.e7.

[142] Chen PJ, Liu DR. Prime editing for precise and highly versatile genome manipulation. Nat Rev Genet 2023;24:161–77.

[143] Flanigan KM, Dunn DM, von Niederhausern A, et al; United Dystrophinopathy Project Consortium. Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort. Hum Mutat 2009;30: 1657–66.

[144] Anzalone AV, Gao XD, Liu DR et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol 2022;40:731–40.

[145] Zhou M, Tang S, Duan N, et al. Targeted-deletion of a tiny sequence via prime editing to restore SMN expression. Int J Mol Sci 2022;23:7941.

[146] Zheng C, Liang SQ, Liu B, et al. A flexible split prime editor using truncated reverse transcriptase improves dual-AAV delivery in mouse liver. Mol Ther 2022;30:1343–51.

[147] Yuan Q, Gao X. Multiplex base- and prime-editing with drive-and-process CRISPR arrays. Nat Commun 2022;13:2771.

[148] Carlson-Stevermer J, Das A, Abdeen AA, et al. Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nat Commun 2020;11:627.

[149] Seshagiri S, Stawiski EW, Durinck S, et al. Recurrent R-spondin fusions in colon cancer. Nature 2012;488:660–4.

[150] Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330–7.

[151] Loveless TB, Grotts JH, Schechter MW, et al. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nat Chem Biol 2021;17:739–47.

[152] Ma H, Tu LC, Naseri A, et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 2016;34:528–30.

[153] Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 2010;64:475–93.

[154] Davidsohn N, Pezone M, Church GM, et al. A single combination gene therapy treats multiple age-related diseases. Proc Natl Acad Sci U S A 2019;116:23505–11.

[155] Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006;126:663–76.

[156] Kalhor R, Kalhor K, Church GM, et al. Developmental barcoding of whole mouse via homing CRISPR. Science 2018;361:eaat9804.

[157] Lu Y, Brommer B, Tian X, et al. Reprogramming to recover youthful epigenetic information and restore vision. Nature 2020;588:124–9.

[158] Goyon A, Yehl P, Zhang K. Characterization of therapeutic oligonucleotides by liquid chromatography. J Pharm Biomed Anal 2020;182:113105.

[159] Stein CA, Castanotto D. FDA-approved oligonucleotide therapies in 2017. Mol Ther 2017;25:1069–75.

[160] Lam JK, Chow MY, Zhang Y, et al. siRNA Versus miRNA as therapeutics for gene silencing. Mol Ther Nucleic Acids 2015;4:e252.

[161] Burnett JC, Rossi JJ. RNA-based therapeutics: current progress and future prospects. Chem Biol 2012;19:60–71.

[162] Rinaldi C, Wood MJA. Antisense oligonucleotides: the next frontier for treatment of neurological disorders. Nat Rev Neurol 2018;14:9–21.

[163] Weng Y, Xiao H, Zhang J, et al. RNAi therapeutic and its innovative biotechnological evolution. Biotechnol Adv 2019;37:801–25.

[164] Alshaer W, Zureigat H, Al Karaki A, et al. siRNA: mechanism of action, challenges, and therapeutic approaches. Eur J Pharmacol 2021;905:174178.

[165] Hossain DM, Dos Santos C, Zhang Q, et al. Leukemia cell-targeted STAT3 silencing and TLR9 triggering generate systemic antitumor immunity. Blood 2014;123:15–25.

[166] Sun Y, Yu D, Geng X, et al. Artificial base-directed in vivo assembly of an albumin–siRNA complex for tumor-targeting delivery. ACS Appl Mater Interfaces 2023;15:8872–83.

[167] Wasungu L, Hoekstra D. Cationic lipids, lipoplexes and intracellular delivery of genes. J Control Release 2006;116:255–64.

[168] Szoka F Jr, Papahadjopoulos D. Procedure for preparation of liposomes with large internal aqueous space and high capture by reversephase evaporation. Proc Natl Acad Sci U S A 1978;75:4194–8.

[169] Zhang S, Xu Y, Wang B, et al. Cationic compounds used in lipoplexes and polyplexes for gene delivery. J Control Release 2004;100: 165–80.

[170] Hoy SM. Patisiran: first global approval. Drugs 2018;78:1625–31.

[171] Hong DS, Kang YK, Borad M, et al. Phase 1 study of MRX34, a liposomal miR-34a mimic, in patients with advanced solid tumours. Br J Cancer 2020;122:1630–7.

[172] Dias N, Stein CA. Antisense oligonucleotides: basic concepts and mechanisms. Mol Cancer Ther 2002;1:347–55.

[173] Mulamba GB, Hu A, Azad RF, et al. Human cytomegalovirus mutant with sequence-dependent resistance to the phosphorothioate oligonucleotide fomivirsen (ISIS 2922). Antimicrob Agents Chemother 1998;42:971–3.

[174] Hoy SM. Nusinersen: first global approval. Drugs 2017;77:473–9.

[175] Syed YY. Eteplirsen: first global approval. Drugs 2016;76:1699–704.

[176] Talap J, Zhao J, Shen M, et al. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021;206:114368.

[177] Khoshnood S, Ghanavati R, Shirani M, et al. Viral vector and nucleic acid vaccines against COVID-19: a narrative review. Front Microbiol 2022;13:984536.

[178] Dey A, Chozhavel Rajanathan TM, Chandra H, et al. Immunogenic potential of DNA vaccine candidate, ZyCoV-D against SARS-CoV-2 in animal models. Vaccine 2021;39:4108–16.

[179] Akiyama H, Kakiuchi S, Rikitake J, et al. Immune thrombocytopenia associated with Pfizer-BioNTech’s BNT162b2 mRNA COVID-19 vaccine. IDCases 2021;25:e01245.

[180] Corbett KS, Werner AP, Connell SO, et al. mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Nat Immunol 2021;22:1306–15.

[181] Sahin U, Oehm P, Derhovanessian E, et al. An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma. Nature 2020;585:107–12.

[182] Rojas LA, Sethna Z, Soares KC, et al. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 2023;618:144–50.

[183] Cubillos-Ruiz A, Collins JJ, Lu TK, et al. Engineering living therapeutics with synthetic biology. Nat Rev Drug Discov 2021;20: 941–60.

[184] Li HS, Wong NM, Tague E, et al. High-performance multiplex drug-gated CAR circuits. Cancer Cell 2022;40:1294–1305.e4.

[185] Sun Y, Yuan Y, Zhang B, et al. a new approach for the treatment of autoimmune diseases. Sci China Life Sci. 2023;66:711–28.

[186] Roybal KT, Rupp LJ, Morsut L, et al. Precision tumor recognition by T cells with combinatorial antigen-sensing circuits. Cell 2016;164:770–9.

[187] Lee S, Khalil AS, Wong WW. Recent progress of gene circuit designs in immune cell therapies. Cell Syst 2022;13:864–73.

[188] Cho JH, Collins JJ, Wong WW. Universal chimeric antigen receptors for multiplexed and logical control of T cell responses. Cell 2018;173:1426–1438.e11.

[189] Lajoie MJ, Boyken SE, Salter AI, et al. Designed protein logic to target cells with precise combinations of surface antigens. Science 2020;369:1637–43.

[190] Kosti P, Opzoomer JW, Larios-Martinez KI, et al. Hypoxia-sensing CAR T cells provide safety and efficacy in treating solid tumors. Cell Rep Med 2021;2:100227.

[191] Lin X, Lee S, Sharma P, et al. Summary of US food and drug administration Chimeric Antigen Receptor (CAR) T-cell biologics license application approvals from a statistical perspective. J Clin Oncol 2022;40:3501–9.

[192] Yeh MT, Bujaki E, Dolan PT, et al. Engineering the live-attenuated polio vaccine to prevent reversion to virulence. Cell Host Microbe 2020;27:736–751.e8.

[193] Graubner UB, Liese J, Belohradsky BH. Impfungen [Vaccination]. Klin Padiatr 2001;213:A77–83. German.

[194] Tell JG, Coller BG, Dubey SA, et al. Environmental risk assessment for rVSVΔG-ZEBOV-GP, a genetically modified live vaccine for ebola virus disease. Vaccines 2020;8:779.

[195] Eto A, Saito T, Yokote H, et al. Recent advances in the study of live attenuated cell-cultured smallpox vaccine LC16m8. Vaccine 2015;33:6106–11.

[196] Syomin BV, Ilyin YV. Virus-like particles as an instrument of vaccine production. Mol Biol 2019;53:323–34.

[197] Ghattas M, Dwivedi G, Lavertu M, et al. Vaccine technologies and platforms for infectious diseases: current progress, challenges, and opportunities. Vaccines 2021;9:1490.

[198] Ma Y, Mao G, Yang W, et al. Studying bona fide SARS-CoV-2 biology in a BSL-2 biosafety environment using a split-virus-genome system. Sci China Life Sci. 2022;65:1894–7.

[199] Charlton Hume HK, Vidigal J, Carrondo MJT, et al. Synthetic biology for bioengineering virus-like particle vaccines. Biotechnol Bioeng 2019;116:919–35.

[200] Tabebordbar M, Lagerborg KA, Stanton A, et al. Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. Cell 2021;184:4919–4938.e22.

[201] Kreitz J, Friedrich MJ, Guru A, et al. Programmable protein delivery with a bacterial contractile injection system. Nature 2023;616: 357–64.

[202] Graur D, Zheng Y, Azevedo RB. An evolutionary classification of genomic function. Genome Biol Evol 2015;7:642–5.

[203] Bamford DH, Grimes JM, Stuart DI. What does structure tell us about virus evolution? Curr Opin Struct Biol 2005;15:655–63.

[204] Ma C-C, Wang Z-L, Xu T, et al. The approved gene therapy drugs worldwide: from 1998 to 2019. Biotechnol Adv 2020;40:107502.

[205] Wu Z, Asokan A, Samulski RJ. Adeno-associated virus serotypes: vector toolkit for human gene therapy. Mol Ther 2006;14:316–27.

[206] Pearson S, Jia H, Kandachi K. China approves first gene therapy. Nat Biotechnol 2004;22:3–4.

[207] Zhang WW, Li L, Li D, et al. The first approved gene therapy product for cancer Ad-p53 (Gendicine): 12 years in the clinic. Hum Gene Ther 2018;29:160–79.

[208] Zhao Z, Anselmo AC, Mitragotri S. Viral vector-based gene therapies in the clinic. Bioeng Transl Med 2021;7:e10258.

[209] Bach PB, Giralt SA, Saltz LB. FDA approval of tisagenlecleucel: promise and complexities of a $475 000 cancer drug. JAMA 2017;318:1861–2.

[210] Mahoney ALG, Nassif NT, O’Brien BA, et al. Viral vectors in gene therapy and clinical applications. Molecular Cloning. IntechOpen 2022;3:1–16.

[211] Li X, Le Y, Yang X, et al. Viral vector-based gene therapy. Int J Mol Sci 2023;24:7736.

[212] Strathdee SA, Hatfull GF, Mutalik VK, et al. Phage therapy: from biological mechanisms to future directions. Cell 2023;186:17–31.

[213] Ye M, Su JQ, An XL, et al. Silencing the silent pandemic: eliminating antimicrobial resistance by using bacteriophages. Sci China Life Sci. 2022;65:1890–3.

[214] Żaczek M, Górski A, Weber-Dąbrowska B, et al. A thorough synthesis of phage therapy unit activity in Poland—its history, milestones and international recognition. Viruses 2022;14:1170.

[215] Lenneman BR, Fernbach J, Loessner MJ, et al. Enhancing phage therapy through synthetic biology and genome engineering. Curr Opin Biotechnol 2021;68:151–9.

[216] Yehl K, Lemire S, Yang AC, et al. Engineering phage host-range and suppressing bacterial resistance through phage tail fiber mutagenesis. Cell 2019;179:459–469.e9.

[217] Jin M, Chen J, Zhao X, et al. An engineered λ phage enables enhanced and strain-specific killing of enterohemorrhagic Escherichia coli. Microbiol Spectr 2022;10:e0127122.

[218] Fan JX, Niu MT, Qin YT, et al. Progress of engineered bacteria for tumor therapy. Adv Drug Deliv Rev 2022;185:114296.

[219] Cavazzana-Calvo M, Thrasher A, Mavilio F. The future of gene therapy. Nature 2004;427:779–81.

[220] Maman S, Witz IP. A history of exploring cancer in context. Nat Rev Cancer 2018;18:359–76.

[221] Park SH, Zheng JH, Nguyen VH, et al. RGD peptide cell-surface display enhances the targeting and therapeutic efficacy of attenuated salmonella-mediated cancer therapy. Theranostics 2016;6: 1672–82.

[222] Chien T, Harimoto T, Kepecs B, et al. Enhancing the tropism of bacteria via genetically programmed biosensors. Nat Biomed Eng 2022;6:94–104.

[223] Lynch J, González-Prieto CC, Reeves A, et al. Engineered E. coli for the targeted deposition of therapeutic payloads to sites of disease. Research Square 2022 (in print). https://doi.org/10.21203/rs.3.rs-1233122/v1

[224] Duong MT, Qin Y, You SH, et al. Bacteria-cancer interactions: bacteria- based cancer therapy. Exp Mol Med 2019;51:1–15.

[225] Loeffler M, Le’Negrate G, Krajewska M, et al. Salmonella typhimurium engineered to produce CCL21 inhibit tumor growth. Cancer Immunol Immunother 2009;58:769–75.

[226] Tanna T, Ramachanderan R, Platt RJ. Engineered bacteria to report gut function: technologies and implementation. Curr Opin Microbiol 2021;59:24–33.

[227] Long Q, Zheng P, Zheng X, et al. Engineered bacterial membrane vesicles are promising carriers for vaccine design and tumor immunotherapy. Adv Drug Deliv Rev 2022;186:114321.

[228] Shen Y, Giardino Torchia ML, Lawson GW, et al. Outer membrane vesicles of a human commensal mediate immune regulation and disease protection. Cell Host Microbe 2012;12:509–20.

[229] Wu S, Yang S, Wang M, et al. Quorum sensing-based interactions among drugs, microbes, and diseases. Sci China Life Sci. 2023;66:137–51.

[230] Thompson JA, Oliveira RA, Djukovic A, et al. Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. Cell Rep 2015;10:1861–71.

[231] Din MO, Danino T, Prindle A, et al. Synchronized cycles of bacterial lysis for in vivo delivery. Nature 2016;536:81–5.

[232] Liao MJ, Din MO, Tsimring L, et al. Engineered population dynamics increase genetic stability. Science 2019;365:1045–9.

[233] Niu D, Church GM, Yang L, et al. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 2017;357:1303–7.

[234] Yang L, Güell M, Church G, et al. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 2015;350:1101–4.

[235] Längin M, Mayr T, Reichart B, et al. Consistent success in life- supporting porcine cardiac xenotransplantation. Nature 2018;564:430–3.

[236] The gene-edited pig heart given to a dying patient was infected with a pig virus. www.technologyreview.com/2022/05/04/1051725/xenotransplant-patient-died-received-heart-infected-with-pig-virus/ (5 May 2022, date last accessed).

[237] Tang H, Abouleila Y, Si L, et al. Human organs-on-chips for virology. Trends Microbiol 2020;28:934–46.

[238] Wang Y, Wang P, Qin J. Human organoids and organs-on-chips for addressing COVID-19 challenges. Adv Sci 2022;9:e2105187.

[239] Zhang M, Wang P, Luo R, et al. Biomimetic human disease model of SARS-CoV-2-induced lung injury and immune responses on organ chip system. Adv Sci 2020;8:2002928.

[240] Si L, Bai H, Rodas M, et al. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics. Nat Biomed Eng 2021;5:815–29.

[241] Aref AR, Huang RY, Yu W, et al. Screening therapeutic EMT blocking agents in a three-dimensional microenvironment. Integr Biol 2013;5:381–9.

[242] Xu H, Li Z, Yu Y, et al. A dynamic in vivo-like organotypic blood-brain barrier model to probe metastatic brain tumors. Sci Rep 2016;6:36670.

[243] Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nat Rev Microbiol 2014;12:381–90.

[244] Rasool A, Jiang Q, Wang Y, et al. Evolutionary approach to construct robust codes for DNA-based data storage. Front Genet 2023;14:1158337.

[245] Boeke JD, Church G, Hessel A, et al. Genome engineering. The genome project-write. Science 2016;353:126–7.

[246] Walde P. Building artificial cells and protocell models: experimental approaches with lipid vesicles. Bioessays 2010;32:296–303.

[247] Zhang XE, Liu C, Dai J, et al. Enabling technology and core theory of synthetic biology. Sci China Life Sci. 2023;66:1742–85.

[248] Wu K, Rao CV. Computational methods in synthetic biology: towards computer-aided part design. Curr Opin Chem Biol 2012;16:318–22.

[249] Matsuura S, Ono H, Kawasaki S, et al. Synthetic RNA-based logic computation in mammalian cells. Nat Commun 2018;9:4847.

[250] Manzoni R, Urrios A, Velazquez-Garcia S, et al. Synthetic biology: insights into biological computation. Integr Biol 2016;8:518–32.

[251] Cramer P. AlphaFold2 and the future of structural biology. Nat Struct Mol Biol 2021;28:704–5.

[252] Humphreys IR, Pei J, Baek M, et al. Computed structures of core eukaryotic protein complexes. Science 2021;374:eabm4805.

[253] Anishchenko I, Pellock SJ, Chidyausiku TM, et al. De novo protein design by deep network hallucination. Nature 2021;600:547–52.

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