1. Introduction
The ongoing evolution of global infectious diseases underscores the increasing necessity and criticality of vaccine development. As an emerging vaccine technology, mRNA vaccines, which utilize the intrinsic mechanisms of human cells to produce specific pathogen antigens, provide a new direction for vaccine development. Properly designed mRNA sequences can enhance the targeting and stability of mRNA vaccines, thereby improving their efficacy and durability [
1]. Traditional non-replicating mRNA vaccines typically comprise a 5′ cap structure, a 5′-untranslated region (UTR), an open reading frame (ORF) encoding the target antigen, a 3′-UTR, and a poly(A) tail structure [
2]. UTRs are critical factors that regulate mRNA stability and translation efficiency, playing significant roles in cellular transcription and translation processes [
3]. In mRNA vaccine design, the selection of UTRs directly impacts the expression levels of the vaccine and may also modulate its immunogenicity [
4,
5,
6]. UTRs may be derived from naturally occurring UTRs of highly expressed genes, such as the UTRs from α- and β-globin genes, as demonstrated in the selection made for the SARS-CoV-2 vaccine BNT162b2 [
7]. Alternatively, UTRs from the pathogen itself can be employed, or advantageous UTRs can be identified through systematic evolution and high-throughput screening, facilitated by artificial intelligence (AI) tools [
8,
9]. However, considering the variability in UTR efficacy across different cell types, there arises a critical need for the development of alternative UTR sequences optimized for specific application needs and intended cellular targets [
10,
11].
The efficacy of the adaptive immune response to pathogens and vaccines is intricately linked to the activation and functionality of dendritic cells (DCs). Serving as sentinel cells, DCs undertake the critical task of surveilling the body for pathogens and vaccine components. Upon encountering these entities, DCs efficiently process antigens and, subsequently, migrate to adjacent lymph nodes via the lymphatic system. Within the lymph nodes, DCs orchestrate the presentation of processed antigens to other immune cells, thereby orchestrating the initiation of a targeted and adaptive immune response tailored to the encountered threat [
12]. DCs are a population of specialized antigen-presenting cells (APCs) consisting of different subtypes, among which immature DCs exhibit a high migratory capacity, while mature DCs can effectively activate naïve T cells, playing a crucial role in initiating, modulating, and maintaining immune responses [
13]. Following the intramuscular administration of lipid nanoparticle (LNP)-mRNA vaccines, neutrophils, monocytes, and dendritic cells (DCs) are recruited to the injection site, where they produce inflammatory secretory factors, including chemokines and other inflammatory mediators. These factors facilitate the extravasation of immune cells. Subsequently, antigen-presenting cells (APCs), especially DCs, effectively uptake and translate the LNP-mRNA, migrate to the nearby lymph node, and enhance antigen presentation, thereby promoting an adaptive immune response [
14,
15]. Targeting the antigen to DCs increases antibody levels [
16]. Dendritic cells in the peripheral blood such as plasmacytoid dendritic cells produce large amounts of type 1 interferon in response to microbial, especially viral, infections and stimulate the corresponding T-cell response [
17]. These dendritic cells can be transported to various tissues and organs in the human body through blood circulation [
18]. Therefore, we hypothesized that optimizing the mRNA sequence to enhance its stability and translation efficiency in peripheral blood dendritic cells could improve the efficacy and durability of mRNA vaccines. In this study, we conducted a screening of untranslated regions (UTRs) derived from highly mRNA-abundant genes in peripheral blood dendritic cells using a bioinformatics analysis. We discovered that the expression of reporter genes in peripheral blood dendritic cells was amplified when utilizing both the 5′UTR and 3′UTR of TMSB10. Subsequently, we employed LNP encapsulation to deliver the SARS-CoV-2 RBD antigen modified with the UTR of TMSB10 and immunized mice via the intramuscular route. Our findings demonstrated that the modified RBD antigen enhanced antigen-specific humoral and T-cell immunity. This investigation highlights the potential of the original UTR of TMSB10 to enhance the immunogenicity of mRNA vaccines, offering promise for diverse applications in the development of viral mRNA vaccines.
2. Materials and Methods
2.1. Molecular Cloning and mRNA Synthesis
The plasmid sequence was designed using Gaussia luciferase (GLuc) reporter gene as the open reading frame (ORF) whose signal peptide was replaced by tissue plasminogen activator (tPA) signal peptide, with the 5′UTR and 3′UTR derived from different genes, followed by the addition of the T7 promoter sequence before the 5′UTR (sequences showed in
Supplementary Table S1). The plasmids were synthesized by GenScript (Nanjing, China) and cloned into pUC57 vector. mRNA was produced using T7 High-Yield RNA Transcription kit (Novoprotein, Shanghai, China) on linearized plasmids. Then, Cap 1 was added to the synthesized RNA by using the Cap 1 Capping System (Novoprotein, Shanghai, China) and Pseudo-UTP (Ψ-UTP, APExBIO, Houston, TX, USA) was fully substituted for UTP. The Poly(A) tails were added using
E. coli Poly(A) Polymerase (Novoprotein, Shanghai, China).
2.2. Cell Culture and Transfection
The HEK 293T cell, DC2.4, or RAW264.7 cell lines were purchased from Biospes Company (Chongqing Biospes Co., Ltd., Chongqing, China). Human bronchial epithelial cell line, 16HBE14o- Human Bronchial Epithelial Cell Line (16HBE), was purchased from Sigma (Sigma-Aldrich, St. Louis, MA, USA). In vitro transient transfection of mRNA was conducted in HEK 293T cells, DC2.4, 16HBE, or RAW264.7 using Lipofectamine® 3000 reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Briefly, HEK 293T cells and RAW264.7 were cultured in DMEM (Gibco, Billings, MT, USA), while DC2.4 and 16HBE were cultured in RPMI 1640, supplemented with 10% FBS (Gibco, Billings, MT, USA) and 1% penicillin-streptomycin (Gibco, Billings, MT, USA). Cell dissociation was achieved using 0.25% TrypLE (Thermo Fisher Scientific, Waltham, MA, USA), and cells were seeded in 48-well plates at a density of 50,000 cells per well. After 18 h, the medium was replaced with 2% FBS-medium, and cells were transfected with mRNA (0.25 μg per well) using Lipofectamine 3000 Transfection Reagent. Supernatants were collected 24 h post-transfection and stored at −80 °C.
2.3. Gaussia Luciferase (GLuc) Assay In Vitro
In vitro evaluation of GLuc expression was conducted using the Secrete-Pair™ Gaussia Luciferase Assay Kit (GeneCopoeia, LF062, Rockville, MD, USA). After thawing the collected supernatant on ice, 10 μL of the supernatant was added to a black 96-well plate for measurement. A working solution was prepared according to the kit instructions (100 μL per well), and the chemiluminescence value was measured at 500 ms using a Varioskan Lux (Thermo Scientific, Waltham, MA, USA).
2.4. Preparation of Lipid-GLuc mRNA Nanoparticles
In brief, SM-102 (AVT, Shanghai, China), DSPC (AVT, Shanghai, China), cholesterol (AVT, Shanghai, China), and DMG-PEG2000 (AVT, Shanghai, China) were dissolved in ethanol at a molar ratio of 50:10:38.5:1.5. And the final concentrations were 26.33 mg/mL for SM-102, 5.86 mg/mL for DSPC, 2.79 mg/mL for DMG-PEG2000, and 11.04 mg/mL for cholesterol. The lipid solution was, then, prepared by mixing SM-102, DSPC, DMG-PEG2000, and cholesterol solution in a 1:1:1:1 volume ratio. The mRNA was solubilized in 50 mM citrate buffer (pH 4.0) with concentration of 0.17 mg/mL. Then, 1 mL of lipid and 3 mL of mRNA solution (N:P ratio of 6:1) are mixed at room temperature through a dual-channel syringe pump at a flow rate of 1:3 (2 mL/min:6 mL/min) through the SCARM Mixer (Shuogen Technology Co., Ltd., Dongguan, China) to form nanoparticles of approximately 100 nm in diameter. The calculation formula of the N:P ratio is as follows:
N provided by SM-102. The molar concentration of SM102 in lipid solution is 9.267 mmol/mL. And the P is from the phosphate group of the RNA bases. The average molecular weight of the RNA bases (324.5 g/mol) was used to calculate the P.
The amount of substance (
n) N:
CN: the concentration of the SM102
The amount of substance P:
C
P: the concentration of the mRNA
LNP-encapsulated mRNA samples were dialyzed against PBS (pH 7.4) in dialysis bags (Viskase, Lombard, IL, USA) for 24 h and stored at 4 °C until use. Encapsulation efficiency was measured using the Quant-iT RiboGreen RNA Assay Kit (Invitrogen, Carlsbad, CA, USA) with a Varioskan Lux (Thermo Scientific, Waltham, MA, USA).
2.5. Gaussia Luciferase (GLuc) Assay In Vivo
LNPs for in vivo imaging were formulated with mRNA encoding Gaussia luciferase (GLuc). The formulated LNPs were administered intramuscularly to mice at a dose of 5 μg of GLuc. Six hours later, tail blood samples were collected from the mice, and the fluorescence value of whole blood was measured using the Secrete-Pair™ Gaussia Luciferase Assay Kit (GeneCopoeia, LF062, Rockville, MD, USA), following the instructions provided. Following blood collection, coelenterazine was injected intraperitoneally immediately and incubated for 5 min. Luciferase expression in different organs was confirmed using an IVIS (PerkinElmer, Waltham, MA, USA).
2.6. Immunization and Detection of Antigen-Specific Antibodies in Mice
Female BALB/c mice were obtained from the Animal Center of the Third Military Medical University, and the animal experiments were ethically approved by the Laboratory Animal Welfare and Ethics Committee of the Third Military Medical University (Approval No. AMUWE20201373). For vaccinations, groups of 6- to 8-week-old BALB/c mice were immunized on days 0 and 7. The mRNA vaccine and the empty carrier control group were administered via intramuscular injection. Each dose of the mRNA vaccine contained 15 μg of mRNA, approximately 100 μL for two thighs. The empty LNP (PBS-LNP) was used as the control. After 14 days post-immunization, 100 μL of blood was collected from the mouse tail vein, followed by centrifugation at 4 °C for 10 min at 3000 rpm to isolate the serum. The serum was subsequently stored at −80 °C until further analysis. The Mice anti-SARS-CoV-2 (S-RBD) IgG ELISA Kit (FineTesT, Wuhan, China) was employed to measure antibody concentrations. Absorbance at 450 nm was measured using Varioskan Lux (Thermo Scientific, Waltham, MA, USA).
2.7. Enzyme-Linked Immunospot (ELISPOT) Assays
Cellular immune responses in vaccinated mice were evaluated using IFN-γ and IL-4 pre-coated ELISPOT kits (MabTech, Hamburg, Germany). According to the instructions, plates were first blocked with 10% FBS in RPMI 1640 (Thermo Fisher Scientific, Waltham, MA, USA) and incubated for 30 min. Then, 1,000,000 splenocytes cells of the immunized mice were seeded in each well and inoculated along with a pool of SARS-CoV-2 RBD peptides (2 mg/mL of each peptide) [
19]. After incubation at 37 °C with 5% CO
2 for 36 h, the plates were washed with wash buffer, and biotinylated anti-mouse IFN-γ and IL-4 antibodies were added to each well, followed by a 2 h incubation at room temperature. Subsequently, AEC substrate solution was added, and, after air-drying, the plates were read using an automated ELISPOT reader (AID Classic EliSpot Reader, Strassberg, Germany). The numbers of spot-forming cells (SFC) per 1,000,000 cells were calculated.
2.8. Flow Cytometry Analyses for Mouse Splenocytes
Evaluation of T cell proliferation in immunized mice was conducted using a FACSCalibur flow cytometer (BD Biosciences, Milpitas, CA, USA). Briefly, a total of 1,000,000 mouse splenocytes were stimulated with the SARS-CoV-2 RBD peptides pool (4 μg/mL of each peptide) for 4 h at 37 °C with 5% CO2. Brefeldin A (1 mg/mL, BD Sciences, Milpitas, CA, USA) was, then, added to the splenocytes and incubated for an additional 4 h. The splenocytes were washed twice with the PBS, and then stained with fluorescently conjugated antibodies to CD3-FITC (BD Pharmingen, San Diego, CA, USA), CD4 (PerCP-Cyanine5.5, BD Pharmingen, San Diego, CA, USA), CD8-PE-Cyanine7 (BD Pharmingen, San Diego, CA, USA), CD44-APC (BD Pharmingen, San Diego, CA, USA), and CD62L-PE (BD Pharmingen, San Diego, CA, USA). Zombie NIR™ Fixable Viability Kit (BioLegend, San Diego, CA, USA), whose stain has similar emission to APC/Cy7, was used to evaluate live or dead status of mammalian cells. Data were analyzed using FlowJo software (Version 10.8.1).
2.9. Data Analysis
All statistical analyses were conducted using GraphPad Prism V8.0.2 software. The Student’s t-test and one-way ANOVA with multiple comparisons tests were employed for statistical comparisons between groups. A p-value ≤ 0.05 was considered indicative of a significant difference between groups.
4. Discussion
Dendritic cells are a specialized class of antigen-presenting cells that play a key role in the immune system [
20]. In this paper, we screened the nine genes with the highest mRNA abundance in each dendritic cell subtype (
Figure 1). Among these genes, TMSB4X, B2M, and TMSB10, namely, which exhibited a high expression in dendritic cells, were ultimately selected (
Figure 2). Notably, the UTR of TMSB10 demonstrated a comparable efficacy in antigen-presenting cells to the previously reported optimized R27-UTR, particularly in DC2.4 cells (
Figure 3a), indicating that the UTR of TMSB10 exhibits a greater efficiency for DC cells. Subsequent animal experiments revealed that the TMSB10 UTR demonstrated elevated expression levels in the bloodstream. Given that TMSB10 was initially identified as a highly expressed gene in peripheral blood cells, its UTR performance corresponds well with its source (
Figure 3b). Subsequently, we applied it to the mRNA vaccine against COVID-19. The experimental results further demonstrated that the UTR of TMSB10 indeed elicits a higher humoral immunity (
Figure 4b) and induces stronger T-cell immune responses (
Figure 4c–g). These findings underscore the feasibility of our approach targeting DCs to design UTRs for enhancing their antigen-presenting capabilities. That is not only applicable to SARS-CoV-2, but also to other mRNA vaccines, thus offering broad prospects for application.
However, these natural UTRs, which have the highest mRNA abundance in antigen-presenting cells, still have room for further improvement. For instance, the TOP motif, a cis-regulatory RNA element, initiates immediately following the m7G cap structure and features a characteristic invariant 5′-cytidine, followed by a continuous stretch of 4–15 pyrimidines [
21]. It is known to negatively regulate mRNA translation [
22]. Upstream open reading frames (uORFs) within the 5′UTR region also serve to suppress downstream protein expression [
23]. Potential enhancements could include the deletion of the 5′ Terminal OligoPyrimidine (5′ TOP) motif or upstream open reading frames (uORFs) in the 5′UTR. Another strategy involves incorporating aptamers into the 5′UTR sequence to recruit translation-enhancing proteins or cap-binding proteins, thereby boosting the expression levels of downstream genes [
24]. Additionally, strategies could include deleting binding sites in the 5′ and 3′UTRs for microRNAs that degrade mRNAs or inhibit their translation [
25,
26], or reducing unstructured sequences within the 3′UTR sequence, among other approaches, all of which have the potential to further enhance the protein translation efficiency [
27]. Alternatively, we can employ AI for genetic evolutionary training using our existing library of highly expressed UTRs to further enhance their expression capabilities [
28]. In addition, the UTR can have a profound effect on mRNA stability, translation, and localization by interacting with various cellular components such as RNA-binding proteins, microRNAs, and RNA structural units. To improve the specificity of UTR targeting to DC cells, we can also add DC-cell-specific regulatory elements to the UTR according to the characteristics of RNA-binding proteins in DC cells. These improvements provide new strategic directions for improving mRNA vaccine efficiency and persistence.
Furthermore, TMSB10 is identified as a protein potentially implicated in regulating cell migration through its actin-monomer-binding activity. It has been linked to the activation of SARS-CoV-2 and VEGFA-VEGFR2 signaling pathways in both extrafollicular and follicular B cells (
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMSB10&keywords=TMSB10, accessed on 12 January 2024). According to our experimental results, TMSB10 might play a significant role in the body’s immune response; yet, it has been understudied, warranting further investigation.
Our study also has limitations. We did not compare our UTRs with the already marketed Moderna and BioNTech mRNA vaccines’ UTRs. This absence of comparative analysis limits our ability to gauge the relative efficacy and potential advantages of our identified UTRs in relation to those already established in commercial vaccines. However, our aim was to propose a strategy for screening natural UTRs for application in mRNA vaccines to enhance antigen immunogenicity. Therefore, we chose the already reported optimized natural UTR, R27, as a control to validate our strategy. In our next work, we will continue to optimize the UTRs we screened and compare them with those in mRNA vaccines already on the market. Furthermore, in this study, we only explored the mRNA expression abundance of the TMSB10 gene in antigen-presenting cells in peripheral blood. Whether it has the same high mRNA abundance in other cell types or other tissues, and whether its UTR can be applied to other gene therapy fields, still needs further research.