The central dogma of biology, which delineates the flow of genetic information from DNA to RNA to protein, along with the principles of cellular immunology, provides a foundational understanding for harnessing the power of synthetic biology to combat cancer. The application of synthetic biology in the design and production of novel tumor vaccines marks a pivotal advance in the field of cancer immunotherapy. This study delves into the cutting-edge development in the creation of therapeutic tumor vaccines, with a particular focus on two critical components: antigen selection and vaccine design. The request for more precise and effective tumor vaccines has garnered the attention of researchers globally. These vaccines are designed to target tumor-specific antigens or those related to tumor growth and survival pathways. Traditional approaches to antigen selection have typically involved targeting specific genes with tumors. However, the advent of high-throughput sequencing and mass spectrometry has revolutionized this process by enabling the screening of novel antigens, thereby enhancing the precision and immunogenicity of vaccines. In recent years, the landscape of tumor vaccines has been significantly broadened by the engineering of vaccines through various platforms. These include DNA-based vaccines, mRNA vaccines, viral or bacterial vector vaccines, and cell-based vaccines. These innovative approaches offer a stark contrast to traditional peptide vaccines, significantly amplifying the immune response against a variety of tumor types. The versatility of synthetic biology allows for the customization of vaccines to target a wide array of tumor antigens, thereby potentiating a more robust and targeted immune reaction. The progress made in synthetic biology is not only refining existing vaccine strategies but also accelerating the pace of experimental research in tumor vaccines. This rapid advancement holds the promise of continually improving the clinical therapeutic effects of these vaccines. As researchers continue to unravel the complexities of tumor immunology and synthetic biology techniques become more efficient, the intersection of these fields is expected to yield a new generation of tumor vaccines that are not only more effective but also safer and more accessible to patients. In conclusion, the integration of biological knowledge and technological innovation in synthetic biology is transforming the development of tumor vaccines. The focus on optimizing antigen selection and vaccine design is driving the creation of more potent and tailored immunotherapies. It is anticipated that synthetic biology will play an even greater role in enhancing the efficacy of tumor vaccines, offering cancer patients with hope in the ongoing battle against this devastating disease.

Glycoproteins with enveloped viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus, and human immunodeficiency virus (HIV), display a trimeric conformation. Different from the monomeric form, the trimeric proteins exhibit superior immunogenicity. Several trimerization motifs, such as Foldon derived from phage T4 fibritin, have been used to promote the formation of trimeric proteins with natural conformations. Although the Foldon-induced trimeric proteins are stable, their high immunogenicity limits applications in the development of vaccine antigens. In a previous study, we developed a recombinant human collagen type Ⅲ protein and determined its crystal structure, revealing a triple-helix conformation. However, the potential of this recombinant protein as a trimerization motif remained unknown. In this study, we demonstrated that the recombinant humanized type Ⅲ collagen (Rh3C) was able to act as a trimerization motif, facilitating the spontaneous trimer formation of the Rh3C-conjugated receptor-binding domain (RBD) within the spike (S) protein of SARS-CoV-2. This trimeric protein could induce a stronger SARS-CoV-2 RBD-specific IgG, IgG1, and IgG2a immune response, when compared with the monomeric RBD protein in the immunized mice. Notably, the Rh3C-RBD protein, when adjuvanted with the novel STING agonist CF501, also elicited significantly higher neutralizing antibody responses against both the pseudotyped SARS-CoV-2 (D614G) and its variant Omicron (BA.2.2) in the immunized mice. To showcase the broad applications of the Rh3C trimerization motif, we further demonstrated that the Rh3C-conjugated HA1 of the influenza virus could also elicit a stronger antibody response than free HA1. Considering the wide distribution of the Rh3C protein in human bodies, its use as a trimerization motif would not induce an immune response due to immune tolerance, thereby allowing the immune response to concentrate on targeted viral proteins. Therefore, this Rh3C-based trimerization motif holds great potential for the design and optimization of vaccines consisting of trimeric protein antigens.

With the research progress and clinical application of immune checkpoint inhibitors and chimeric antigen receptor T-cell therapies, immunotherapy has substantially changed the treating modalities for various tumors. Tumor neoantigen vaccines, as a promising immunotherapy method, aim to trigger a novel T cell response against neoantigens. Neoantigens, with their high specificity, can induce and expand the tumor-specific T cell receptor repertoire, which were discovered through the second-generation sequencing of DNA extracted from both the patient’s tumor and non-tumor tissue samples. The sequences and HLA types are then analyzed for alignment to pinpoint tumor-specific mutations. To validate the significance of these mutations, RNA sequencing data are integrated with the results. Subsequently, bioinformatics platforms are employed for the prediction and analysis of neoantigens encoded by mutated genes and HLA types, enabling the identification of potential immunogenic neoantigens. Finally, the immunogenicity of these neoantigens is assessed through techniques such as ELISPOT and tetramer assays. Tumor vaccines can be categorized as peptide-based, DNA-based, RNA-based, and DC-based products. Viruses, lipid nanoparticles, and nano delivery systems can activate antigen-presenting cells, enhancing their ability to recognize and present tumor-associated antigens, thus promoting the activation of CD8⁺ T cells. Neoantigen vaccines can be administered through various routes, including subcutaneous injection, intramuscular injection, intraperitoneal injection, intradermal injection, intravenous injection, or intralymphatic injection. Preliminary clinical studies have shown that neoantigen tumor vaccines have demonstrated evidence of strong tumor-specific immunogenicity and antitumor activity. In this review, we summarize in detail the source, prediction, and identification of tumor neoantigens, as well as the classification and immunization scheme of neoantigen vaccines. In addition, we highlight strategies for optimizing tumor neoantigen vaccines, including prediction algorithms, expressing multiple epitope structures, increasing immunogenicity, administration methods and delivery systems, and combining adjuvants and various treatments, providing new insights for the development of personalized immunotherapy.

Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019, it has evolved into different lineages, including Alpha, Beta, Delta, and Omicron. The development of broad-spectrum vaccines has become a necessity for preventing the highly mutated respiratory viruses. Traditional vaccine antigens, originating from prototype strains, cannot cover rapid mutations with these viruses, leading to breakthrough infections. With the development of synthetic biology, new technologies such as multivalent coupling of antigens, reconstructed dominate antigen modules, engineering design of conserved epitopes, epitope display, and computation-guided reconstruction have enabled redesigning antigens to achieve stronger immunogenicity with broader spectrum. The technology of synthetic biology is also applicable in the vaccine production process, such as antigen expression in nanoparticles, viral vectors, nucleic acids, and subunits. This article reviews the applications of synthetic biology technology in developing broad-spectrum vaccines in recent years, particularly for the broad-spectrum SARS-CoV-2 vaccines, and summarizes how to display common antigens and cross-antigenic sites by the reverse vaccinology for the activation of broad-spectrum immune responses against different mutant strains, achieving broad-spectrum vaccine protection effects through “remaining constant in response to ever-changing”. The article also provides a comprehensive comparison of the strengths and limitations of different broad-spectrum vaccine design strategies and discusses challenges to applying synthetic biology in the development of vaccines, offering valuable insights for universal against highly mutation viruses.

Influenza viruses are highly variable and transmissible, and their infections can cause infectious respiratory diseases, such as seasonal influenza outbreaks around the world, one of the most serious public health problems at present, which can be prevented by influenza vaccination. The genome sequences, protein structures and functions of influenza viruses, as well as their packaging mechanisms are relatively clear. they are also important models, which can be used for developing conditional control genetic elements and the construction of intelligent responsive viruses. With the development of reverse genetics and synthetic biology technology, influenza viruses that are genetically engineered can better control virus replication to improve the safety of vaccines, and induce strong immune responses in human being, which have attracted wide attention in tumor immunotherapy. Several studies using simple or modified influenza viruses for treating liver cancer, melanoma, or lung cancer have found breakthroughs. In this paper, three novel strategies for attenuating influenza viruses, namely, proteolytic targeted chimeric virus, conditionally replicating influenza-attenuated live virus and highly interferon-sensitive virus, are described. The oncolytic effects of influenza viruses encoding premature stop codon chimeric antigen peptide, influenza viruses recombining with PD-L1 or CTLA4 immune checkpoint and influenza viruses expressing GM-CSF with truncated NS1 fragment on melanoma and hepatocellular carcinoma are reviewed, respectively, which suggest that the influenza viruses can be used as a live attenuated vaccine and a potential carrier for oncolytic viruses, and future researchers can be focused on constructing influenza viruses with more innovative strategies and different viruses to build a live attenuated vaccine and oncolytic viruses, in order to obtain high safety and more clinical curative treatment, improving the life quality of the patients.

Nanoparticle vaccines have been established firmly as a cornerstone of modern immunization strategies, with a compelling history that trace their pioneering use in human being back to 1981. Within the past four decades, these vaccines have not only demonstrated their efficacy, but have also been developed as powerful tools in fighting against a range of infectious diseases, most notably hepatitis B virus (HBV) and human papillomavirus (HPV). Their success can be attributed to their exceptional immunogenicity and impeccable safety as well, making them invaluable in curbing the spread of viruses and safeguarding the health and well-being of human being. The global outbreaks of the COVID-19 pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has made vaccination into the forefront of public health priorities. This unprecedent challenge has accelerated the progress of various vaccine technologies, with nanoparticle vaccines attracting considerable attention. However, due to their relatively empirical design approaches and complicated manufacturing processes, progress in the clinical trials of SARS-CoV-2 nanoparticle vaccines has not been highlighted particularly. Therefore, the imperative for developing nanoparticle vaccines is to figure out their rational design, requiring groundbreaking advancement in novel technologies and theories. In this endeavor, synthetic biotechnology has emerged as an indispensable tool, driving the technological innovations of the production of nanoparticle vaccines. This article begins with an overview of technological advancements in the development of nanoparticle vaccines, encompassing progress from self-assembled nanoparticles to assist-assembled nanoparticles, and ultimately to antigen-display on formed nanoparticles. Furthermore, discoveries in understanding the unique roles of nanoparticle vaccines in enhancing antigen immunogenicity are updated, particularly in the function of nanoparticles with novel antigen presentation pathways. Finally, a comprehensive summary of the clinical trials of nanoparticle vaccines on fighting the COVID-19 pandemic is presented. In conclusion, we firmly believe that nanoparticle vaccines, bolstered by the scaffolding of synthetic biotechnology, are poised to emerge as steadfast guardians in the global battle against emerging and highly infectious diseases, and ongoing progress in this regard not only holds great promise, but also has potentials to revolutionize contagious disease prevention and control on a global scale.

In recent years, bacterial infections have emerged as the second leading cause of death globally, posing a serious threat to public health and demanding prioritized intervention from the healthcare community worldwide. While antibiotics have conventionally been used as the primary strategy to combat bacterial infections, their efficacy is increasingly compromised due to the emergence of drug-resistant bacteria, especially multi-drug-resistant and even pan-drug-resistant superbacteria. Vaccines are thus considered as one of the most scientific, economical, safe, and effective means to prevent infectious diseases and improve public health, which are estimated to save 2 to 3 million lives annually, and can serve as a critical tool in the battle against antimicrobial resistance. However, the complexity of bacterial structure and pathogenic mechanism has hindered the development of vaccines. Challenges include screening and rationally design of effective antigens, ensuring compatibility of various antigen combinations, establishing animal models for preclinical evaluation, and defining reliable endpoints for clinical efficacy assessment. As a result, only a small number of bacteria vaccines have been successfully developed so far, and none of them has been licensed to combat the most prevalent drug-resistant infections, such as Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae. Synthetic biology is a brand-new multidisciplinary focusing on repurposing natural biological systems and inventing innovative biological tools, technologies, devices, and systems for practical applications, and its concepts, principles and technologies have been extensively employed to facilitate vaccine development, including rational design, screening, and optimization of antigen, carrier, adjuvant and delivery system as well as the modulation of bacterial pathogenicity and immune responses. Herein, we outline the current status of the development of bacterial vaccines and the advancement of clinical trials for drug-resistant bacterial vaccines. Then, we summarize the application of synthetic biology technology in the development of major bacterial vaccines. Finally, we prospect the potential of synthetic biology in creating novel bacterial vaccines. Researchers have access to a greater variety of design possibilities for bacterial vaccines through synthetic biology. To maximize these benefits, we should employ synthetic biology and related technologies more efficiently in developing bacterial vaccines. Meanwhile, we should develop a scientific, reasonable, effective, and feasible management system, as well as regulatory measures, to expedite the development of efficient bacterial vaccines, therefore addressing the problem of antibiotic resistance to protect human health.

Recent outbreaks of infectious diseases, such as the middle east respiratory syndrome, Zika infection, Ebola hemorrhagic fever, and Coronavirus disease (COVID-19) pose significant challenges on the rapid development of efficacious vaccines. Virus-vectored vaccines, as an important new vaccine, can be administrated noninvasively through aerosol inhalation or oral administration, which could stimulate humoral, cellular, and mucosal immune responses without the need for adjuvants, showing good immunogenicity and safety in clinical trials or in emergency use. With the deeper understanding of the viral genome and structural proteins, synthetic biology has enabled the design and modification of viruses to produce recombinant viral vector-based vaccines with high titer, safety, and immunogenicity, and such research has significant implications for the vaccine development. This review highlights major strategies employed in the construction of virus-vectored vaccines, including the construction method of replication-competent or replication-defective viral vectors, and the development of viral vectors commonly used in producing the recombinant vaccines. Among these viral vectors, replication-deficient adenovirus-based vectors with gene deletion in the E1 and E3 regions are most mature for use. Currently, adenoviral vectors that have been used in the approved recombinant vaccines include Ad5, Ad26 and ChAdOx1. Vesicular stomatitis virus and flavivirus with small genomes are negative-sense and positive-sense single-stranded RNA viruses, respectively, which are easy to prepare and more suitable for being used in developing recombinant vaccines with small antigen proteins. Poxviruses and herpesviruses have large genomes for high packing capacity, but they are most difficult to be modified with synthetic biology methods. Different viral vectors need to be prepared using different strategies, and consequently vaccines developed with these vectors have different immune effects. The construction strategies of different viral vector vaccines introduced in this review will provide valuable theoretical reference for the research and development of novel viral vector vaccines. In the future, virus-vectored vaccines will be iteratively developed for higher safety, stronger protection, better compliance and lower production cost.

Cell surface receptors are important membrane proteins that play a crucial role in mediating signal transduction between the intra- and extracellular environments, which sense extracellular chemical or physical stimuli through their extracellular structures to transmit and amplify signals into the cell through their transmembrane domains, ultimately leading to cellular decision-making. Cell surface receptor clustering is a key molecular mechanism for precisely recognizing extracellular signals and initiating internal signaling cascade responses. The clustering and activation of cell surface receptors are essential for various biological processes such as cell migration, proliferation, apoptosis, and differentiation. In addition, mutations in membrane receptors can lead to the abnormal activation of intracellular signaling pathways, contributing to the pathogenesis of various diseases, such as cancer, diabetes, and atherosclerosis. Given the close relevance of receptor-mediated cellular functions to health and disease, researchers have devoted great effort to exploring the biophysical principles of receptor signal transduction and activation, as well as developing diverse molecular engineering strategies for manipulating receptor activation and the corresponding cellular function. With the emergence and rapid development of chemical synthetic biology, molecular engineering tools have been developed, making the rational regulation of receptor activation much simpler as well as more precise and diverse. This review first summarizes the key functional modules involved in regulating receptor clustering, including molecular recognition, spatial organization, dynamics, and cell-selective modules. We then highlight the latest research advances in highly controllable functional modules enabling the artificial engineering of receptor clusters with dynamic aggregation, specific responsiveness, temporal and spatial resolution, and high cell selectivity. Moreover, we emphasize the emerging applications of various precise molecular strategies for artificially controlling receptor clustering to manipulate cellular phenotypes and cell fates, including immune activation and in vivo tissue regeneration. Finally, we perspective the unresolved issues and challenges in developing receptor clustering strategies, pertaining to the mechanisms of receptor clustering, designs of molecular recognition modules, limitations of clinical applications, safety and long-term in vivo uses, and the potential applications of these strategies in disease treatment.

The CRISPR-Cas system consists of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, which has become the focus of molecular diagnosis because it recognizes and cleaves specific DNA or RNA sequences. Using Cas proteins (Cas12, Cas13, Cas14, Cas3, etc.) combined with signal amplification and transformation techniques (fluorescence, potentiometric, colorimetric, lateral flow assay, etc.), researchers have developed many diagnostic platforms with high sensitivity, good specificity, and low cost, which provide a new tool for detecting pathogen nucleic acids. This review presents the biological mechanism and classification of the CRISPR-Cas system, and also summarizes existing technologies for detecting pathogenic nucleic acids based on the trans-cleavage activity of Cas proteins, commenting their properties, functions and application scenarios, with future applications prospected based on the functional characteristics of the CRISPR-Cas system, which is expected to become an ideal detection platform for other multiple targets.