In silico design of a multi-epitope vaccine against the triple negative breast cancer

Triple-negative breast cancer (TNBC) represents a particularly aggressive subtype of breast cancer lacking expression of estrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (HER2), leading to restricted treatment options and unfavorable outcomes and prognosis. This research employs immunoinformatics and reverse vaccinology strategies to develop novel multi-epitope protein and mRNA vaccines targeting TNBC-associated antigens. By using a detailed scoring system, we identified seven extracellular proteins (TROP-2, EpCAM, MUC1, NECTIN4, Folate Receptor α, Mesothelin, α-Lactalbumin) and two intracellular proteins (MAGE-A, NY-ESO-1) as targets for the vaccine. Through a thorough process of predicting and validating epitopes, we discovered 18 MHC-I epitopes, 1 MHC-II epitope, and 2 B-cell epitopes with considerable binding affinity and population coverage (87.75% for the Persian-Iranian cohort), with an emphasis on the MHC-I pathway. The constructed protein vaccine demonstrated favorable physicochemical characteristics, structural stability, non-toxicity, and non-allergenic potential. TLR4 was found to be the primary pattern recognition receptor for adjuvant interaction, and molecular docking illustrated strong binding strength. In constructing the mRNA vaccine, we included N-5' m7GCap, 5' UTR, Kozak sequence, signal peptide (tPA), MHC epitopes, linker, MITD sequence, stop codon, 3' UTR, and poly-A tail. Consequently, the design of the mRNA vaccine integrated optimized codon sequences with relevant regulatory components, achieving a Codon Adaptation Index of 0.93. Furthermore, we propose an innovative four-part mRNA vaccine approach to balance therapeutic effectiveness with clinical practicalities. Both vaccine formulations showed intense immune stimulation in silico, indicating their potential as promising candidates for immunotherapy against TNBC, which will require further experimental exploration.