Design of Personalized Neoantigen RNA Vaccines Against Cancer Based on Next-Generation Sequencing Data. 2022

Begoña Alburquerque-González, and María Dolores López-Abellán, and Ginés Luengo-Gil, and Silvia Montoro-García, and Pablo Conesa-Zamora
Pathology and Histology Department Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Murcia, Spain.

The good clinical results of immune checkpoint inhibitors (ICIs) in recent cancer therapy and the success of RNA vaccines against SARS-nCoV2 have provided important lessons to the scientific community. On the one hand, the efficacy of ICI depends on the number and immunogenicity of tumor neoantigens (TNAs) which unfortunately are not abundantly expressed in many cancer subtypes. On the other hand, novel RNA vaccines have significantly improved both the stability and immunogenicity of mRNA and its efficient delivery, this way overcoming past technique limitations and also allowing a quick vaccine development at the same time. These two facts together have triggered a resurgence of therapeutic cancer vaccines which can be designed to include individual TNAs and be synthesized in a timeframe short enough to be suitable for the tailored treatment of a given cancer patient.In this chapter, we explain the pipeline for the synthesis of TNA-carrying RNA vaccines which encompasses several steps such as individual tumor next-generation sequencing (NGS), selection of immunogenic TNAs, nucleic acid synthesis, drug delivery systems, and immunogenicity assessment, all of each step comprising different alternatives and variations which will be discussed.

UI MeSH Term Description Entries
D007167 Immunotherapy Manipulation of the host's immune system in treatment of disease. It includes both active and passive immunization as well as immunosuppressive therapy to prevent graft rejection. Immunotherapies
D009369 Neoplasms New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms. Benign Neoplasm,Cancer,Malignant Neoplasm,Tumor,Tumors,Benign Neoplasms,Malignancy,Malignant Neoplasms,Neoplasia,Neoplasm,Neoplasms, Benign,Cancers,Malignancies,Neoplasias,Neoplasm, Benign,Neoplasm, Malignant,Neoplasms, Malignant
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000087503 mRNA Vaccines Vaccines formulated with recombinant mRNAs which are taken up by the host cells that translate the mRNA and present the translated proteins to the immune system as antigens in a manner similar to that which would occur during natural infection. This induces humoral and cellular immune responses against the encoded antigen. Messenger RNA Vaccines,Naked RNA Vaccines,RNA Vaccines,Self-Amplifying RNA Vaccine,Trans Amplifying RNA Vaccine,saRNA Vaccine,taRNA Vaccine,RNA Vaccine,mRNA Vaccine,RNA Vaccine, Self-Amplifying,Self Amplifying RNA Vaccine,Vaccine, RNA,Vaccine, Self-Amplifying RNA,Vaccine, mRNA,Vaccine, saRNA,Vaccine, taRNA,Vaccines, RNA
D000951 Antigens, Neoplasm Proteins, glycoprotein, or lipoprotein moieties on surfaces of tumor cells that are usually identified by monoclonal antibodies. Many of these are of either embryonic or viral origin. Neoplasm Antigens,Tumor Antigen,Tumor Antigens,Antigen, Tumor,Antigens, Tumor
D014614 Vaccines, Synthetic Small synthetic peptides that mimic surface antigens of pathogens and are immunogenic, or vaccines manufactured with the aid of recombinant DNA techniques. The latter vaccines may also be whole viruses whose nucleic acids have been modified. Antigens, Synthetic,Chemical Vaccine,Chemical Vaccines,Immunogens, Synthetic,Molecular Vaccine,Molecular Vaccines,Recombinant Vaccine,Semisynthetic Vaccine,Semisynthetic Vaccines,Synthetic Antigen,Synthetic Vaccine,Synthetic Vaccines,Vaccines, Recombinant,Synthetic Antigens,Synthetic Immunogens,Vaccines, Chemical,Vaccines, Molecular,Vaccines, Semisynthetic,Antigen, Synthetic,Recombinant Vaccines,Vaccine, Chemical,Vaccine, Molecular,Vaccine, Recombinant,Vaccine, Semisynthetic,Vaccine, Synthetic
D059014 High-Throughput Nucleotide Sequencing Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc. High-Throughput Sequencing,Illumina Sequencing,Ion Proton Sequencing,Ion Torrent Sequencing,Next-Generation Sequencing,Deep Sequencing,High-Throughput DNA Sequencing,High-Throughput RNA Sequencing,Massively-Parallel Sequencing,Pyrosequencing,DNA Sequencing, High-Throughput,High Throughput DNA Sequencing,High Throughput Nucleotide Sequencing,High Throughput RNA Sequencing,High Throughput Sequencing,Massively Parallel Sequencing,Next Generation Sequencing,Nucleotide Sequencing, High-Throughput,RNA Sequencing, High-Throughput,Sequencing, Deep,Sequencing, High-Throughput,Sequencing, High-Throughput DNA,Sequencing, High-Throughput Nucleotide,Sequencing, High-Throughput RNA,Sequencing, Illumina,Sequencing, Ion Proton,Sequencing, Ion Torrent,Sequencing, Massively-Parallel,Sequencing, Next-Generation
D019496 Cancer Vaccines Vaccines or candidate vaccines designed to prevent or treat cancer. Vaccines are produced using the patient's own whole tumor cells as the source of antigens, or using tumor-specific antigens, often recombinantly produced. Cancer Vaccine,Neoplasm Vaccines,Tumor Vaccine,Tumor Vaccines,Vaccines, Cancer,Vaccines, Neoplasm,Vaccines, Tumor,Vaccine, Cancer,Vaccine, Tumor

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