Genome editing is a type of genetic engineering wherein specific nucleotide(s) in the genome can be precisely edited (inserted, deleted, or replaced). Technologies to manipulate genomes have greatly improved during the last few years. For several decades, scientists have relied upon homologous recombination (HR), a naturally occurring but infrequent event, to introduce or correct DNA alterations at specific genomic loci. Pioneering studies described the recombination and precise insertion of homologous DNA molecules at appropriate chromosomal locations of mammals [1,2]. In 1987, Capecchi's group succeeded in mutating the HPRT gene in ES cells by gene targeting [3]. These early studies were very useful for forecasting and advancing the gene targeting approaches, particularly in mouse embryonic stem (ES) cells. In the early experiments, relatively low efficiency of targeted integration was observed by HR in cultured somatic cell lines (at best 1 in 1000), even after selection. However, the method was more potent as compared to insertion of a genomic DNA fragment into its corresponding chromosomal location by HR via direct pronuclear microinjection of fertilized eggs of the mouse [4]. It showed a promising result that opening the donor DNA molecule using a double-strand break (DSB) within the region of homology greatly increased the frequency of HR within the gene. That is why the benefits for the integration efficiency are somewhat correlated with the promotion of DSBs in the donor DNA template which is exposing homologous sequences at the end of these DNA molecules. This observation would play a major role in succeeding developments leading to the first genome-editing methodologies.

The next step towards the establishment of the first genome-editing methodologies was based on using I-SceI yeast meganuclease which is a rare-cutter endonuclease. However, the procedure was lengthy and difficult to carry out which was required two consecutive HR steps and two markers for selection. These meganucleases were the first to be used for genome-editing purposes, followed by genome-editing nucleases including zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and CRISPR-associated proteins (Cas). The mechanism of these nucleases to enhance gene disruption or HR in the presence of suitable donor DNA molecules is the same where they all efficiently promote DSBs at a specific genomic location. The endogenous cellular repair mechanisms may occur in the absence of homology like in non-homologous end joining (NHEJ) or in the presence of homology like in homology-driven repair (HDR). In HDR in the presence of adequate donor DNA molecules where the homologous sequences surrounding the DSB will seal this breach in the genome. The original DSB can result in gene disruption events depending on the repair route taken by the cells which may be associated with the insertion or deletion of nucleotides (INDELs) via NHEJ or HDR (as shown in the figure below). The quantifiable benefits of these nucleases concerning the increase in the frequency of HR events are estimated to be at least 1000-fold [5]. Fig. 1 illustrates the different approaches developed for genome editing.

Vaccines play a critical role in preventing and controlling infectious diseases [6]. Traditionally, vaccine development has relied on conventional methods such as live-attenuated or inactivated pathogens. However, the advent of genome editing technologies, particularly CRISPR-Cas9, has revolutionized the field by offering new tools and approaches for vaccine design and development. This article explores the use of genome editing in vaccine development and its potential to enhance vaccine efficacy, target specific pathogens, and accelerate the vaccine development process. Genome editing allows for precise modifications of pathogen genomes, enabling the design of vaccines with enhanced efficacy and safety profiles. With CRISPR-Cas9, specific genes or regions of pathogens can be targeted for modification or removal. This approach can eliminate or attenuate virulence factors, making the pathogen less harmful while retaining its immunogenicity. By precisely engineering the genetic makeup of the pathogen, researchers can develop vaccines that elicit robust and specific immune responses, leading to improved protection against the targeted disease. Genome editing enables the optimization of vaccine antigens, the components that stimulate the immune system. By modifying specific amino acid sequences or epitopes within antigens, researchers can enhance their immunogenicity, stability, and ability to induce protective immune responses. Additionally, genome editing techniques can be employed to introduce specific modifications that improve antigen presentation and immune recognition. This tailored approach to antigen optimization holds promise for the development of more effective vaccines.

Many vaccines rely on viral or bacterial vectors to deliver antigens to the immune system. Genome editing techniques allow for the precise modification of these vectors to enhance their safety, immunogenicity, and capacity to deliver antigens. For instance, viral vectors can be engineered to remove pathogenic genes or enhance their immunostimulatory properties. Genome editing also enables the insertion of desired antigens into the vector genome, ensuring efficient expression and presentation to the immune system. These modifications can improve vector stability, reduce vector-associated side effects, and increase the vaccine's overall effectiveness. Genome editing technologies provide insights into the role of specific host genes in vaccine responses. By selectively editing genes involved in the immune response, researchers can gain a deeper understanding of how genetic variations impact vaccine efficacy. This knowledge can guide the development of personalized vaccines or the identification of individuals who may require alternative vaccination strategies. Understanding the interplay between host genetics and vaccine responses may help optimize vaccine regimens and improve overall immunization outcomes. Genome editing can enhance vaccine safety and manufacturing processes. By precisely editing vaccine strains, researchers can eliminate potential safety concerns associated with residual virulence or unwanted genetic modifications.

Additionally, genome editing technologies can be used to streamline the production of vaccines by modifying the genomes of production organisms, optimizing their growth characteristics, and increasing the yield of vaccine antigens. These advancements can improve the efficiency and scalability of vaccine production, making vaccines more accessible and cost-effective.