A comprehensive comparison of DNA and RNA vaccines

Abstract

Nucleic acid technology has revolutionized vaccine development, enabling rapid design and production of RNA and DNA vaccines for prevention and treatment of diseases. The successful deployment of mRNA and plasmid DNA vaccines against COVID-19 has further validated the technology. At present, mRNA platform is prevailing due to its higher efficacy, while DNA platform is undergoing rapid evolution because it possesses unique advantages that can potentially overcome the problems associated with the mRNA platform. To help understand the recent performances of the two vaccine platforms and recognize their clinical potentials in the future, this review compares the advantages and drawbacks of mRNA and DNA vaccines that are currently known in the literature, in terms of development timeline, financial cost, ease of distribution, efficacy, safety, and regulatory approval of products. Additionally, the review discusses the ongoing clinical trials, strategies for improvement, and alternative designs of RNA and DNA platforms for vaccination.

Keywords: COVID-19; Cancer vaccine; Infectious disease; Nucleic acid vaccine.

Figure 1.. Pathways of mRNA and DNA vaccination.

(1) mRNA and DNA vaccines can be administered through intramuscular injection or other methods, after which the vaccine will be internalized by host somatic cells (2). mRNA and DNA vaccines encode genetic information for the antigens and rely on the host’s own protein synthesis machinery to produce the antigens. mRNA needs to be released from its delivery vehicle, e.g., LNP, after entering the host cells and directly translated into the protein antigen. Plasmid DNA vaccine needs to be transported into the cell nucleus before the genetic information in the DNA can be read and transcribed into mRNA. Afterwards, the mRNA exits the nucleus and is translated into the protein antigen being encoded. (3) The synthesized antigen is transferred into antigen-presenting cells (APCs) that migrate to secondary lymphoid organs to (4) activate T cells through interaction between the MHC molecules and T cell receptors (TCR) as well as interaction between the costimulatory molecules, such as CD86 on the surface APC and receptors such as CD28 on T cells. Activated CD4+ T cells secrete proinflammatory cytokines to activate B cells that are responsible for (5) building a humoral immune response against the antigen.

Figure 2.. Production of mRNA and DNA vaccines.

(Left) One common way to produce an mRNA-LNP vaccine. (1) The genetic sequence identified for the target antigen is inserted into a circular DNA vector. (2) Then the circular DNA is amplified in bacteria and isolated. (3) After linearizing the circular DNA template, the genetic sequence is (4) transcribed into mRNA by bacteriophage polymerases in vitro, and (5) the mRNA transcripts are purified by high performance liquid chromatography (HPLC). (6) The mRNA is rapidly mixed with lipids in a microfluidic mixer, resulting in instantaneous encapsulation of mRNA by the lipids and precipitation as self-assembled nanoparticles (mRNA-LNPs). (7) The mRNA-LNP solution is purified through dialysis or filtration to remove non-aqueous solvents and unencapsulated mRNA. (8) The purified mRNA vaccine product is packaged in sterilized vials before use. (Right) One way to produce a DNA vaccine. (1) The genetic sequence identified for the target antigen is inserted into a plasmid DNA vector. (2) Then the plasmid DNA is amplified in bacteria and isolated. (3) After purification of the plasmid DNA by HPLC, (4) the resulted DNA vaccine product is packaged in sterilized vials before use.

Figure 3.. Clinical trials and milestones of mRNA and DNA vaccines for COVID-19.

Pfizer-BioNTech started phase I/II clinical trial for their COVID-19 mRNA vaccine candidate BNT162b2 in April 2020, followed by a phase II/III trial in July 2020. BNT162b2 (commercial name: Comirnaty) is the first COVID-19 vaccine to receive Emergency Use Authorization (EUA) in the U.S. – EUA for adult use was granted in December 2020. Full approval from the FDA was received in August 2021 for use of Comirnaty in individuals 16 years and older. Moderna started phase I clinical trial for their COVID-19 mRNA vaccine candidate mRNA-1273 in March 2020, phase II trial in May 2020, and phase III trial in July 2020. EUA from the U.S. FDA was granted for mRNA-1273 (commercial name: Spikevax) in December 2020, shortly after Comirnaty was authorized for emergency use. Full approval from the FDA was received in January 2022 for use of Spikevax in adults. Indian pharma Zydus Cadila started phase I/II clinical trial for their COVID-19 DNA vaccine candidate ZyCoV-D in July 2020 and phase III trial in January 2021. It received approval of emergency use in restricted situation in India by the Drugs Controller General of India (DCGI) in August 2021.

Figure 4.. Clinical applications of mRNA/DNA vaccine technology.

mRNA and DNA vaccines have been extensively tested in clinical trials for treatment of cancer and prevention of infectious diseases, such as SARS-CoV-2, influenza, respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), Zika virus (ZIKV). mRNA and DNA vaccines currently involved in clinical trials for infectious diseases encode one or a few of proteins (antigens), such as SARS-CoV-2 Spike protein, influenza hemagglutinin (HA), RSV fusion (F) glycoprotein, HIV envelop (Env) protein, pre-membrane and envelope (prME) protein in ZIKV, ZIKV virus-like particle (VLP). For cancer vaccines in current clinical trials, the proteins encoded by mRNA and DNA include personalized neoantigens, oncogenic viral antigens (such as HPV E6 and E7 oncoprotein), and tumor-associated antigens (TAA). Furthermore, mRNA and DNA have been used as genetic adjuvants, encoding cytokines, such as interleukin-12 (IL-12) and GM-CSF, for enhancing immune responses to the antigens.

Figure 5.. Comparison of conventional mRNA vaccine with self-amplifying RNA (saRNA) and circular RNA (circRNA) vaccines.

(A) Conventional mRNA is in a linear format. After mRNA enters the host cells (1), it is used for translation of protein antigen by ribosomes (2). At the same time, due to the linear structure of mRNA, they are susceptible to degradation by nucleases including endonucleases and exonucleases (3). Thus, conventional mRNA has a short half-life in host cells and limited protein antigen expression. (B) saRNAs contain genetically engineered replicons derived from self-replicating single-stranded RNA viruses. After saRNA enters the host cells (1), it undergoes self-amplification in host cells by the RNA-dependent RNA polymerase (RdRP) complex (2). This results in larger amount and longer availability of antigen-coding mRNA in host cells, leading to increased and prolonged protein antigen production (3). Similar to mRNA, saRNA can be degraded by nucleases (4). (C) circRNA is covalently ligated and contains IRES sequence for internal ribosome entry. After circRNA enters the host cells (1), it is used for translation of protein antigen (2). circRNA can be degraded by endonucleases (3) but the degradation is slower than that of mRNAs and saRNAs, due to its covalently closed circular structure (4). As a result, circRNA is more stable and has a longer half-life in host cells. Protein antigens translated from these RNAs will be transferred to antigen presenting cells (not shown in the figure) for processing and presentation on MHC complexes to activate host immune responses. UTR, untranslated region. CDS, coding sequence. IRES, internal ribosome entry site.