Micropeptide colorectal neoplasia differentially expressed (CRNDE) 84aa encoded by CRNDE elicits a T-cell immune response to breast cancer

Background: The activation of anti-tumor immunity by tumor antigens is central to cancer immunotherapy. Cryptic peptides from non-coding regions represent potential antigens, with long non-coding RNAs (lncRNAs) emerging as a novel source of such peptides. This study aims to demonstrate that specific lncRNAs overexpressed in immunologically “cold” tumors—breast cancer, encode immunogenic peptides capable of activating anti-tumor immune responses. Methods: We identified elevated colorectal neoplasia differentially expressed (CRNDE) expression in breast cancer via database mining and polymerase chain reaction (PCR). Plasmid transfection and Western blot confirmed CRNDE peptide production. The immunogenicity of the peptide was assessed by enzyme-linked immunospot (ELISpot) and flow cytometry, while its ability to activate cytotoxic T lymphocytes (CTLs) was evaluated through flow cytometry and lactate dehydrogenase (LDH) release assays. Immunohistochemistry (IHC) and Western blot verified high expression of the CRNDE encodes an 84-amino acid peptide (CRNDE 84aa) peptide in breast cancer. Finally, patient-derived xenograft (PDX) models were used to validate in vivo tumor suppression mediated by CRNDE 84aa-activated CTLs. Results: We demonstrated that lncRNA CRNDE 84aa. A predicted HLA-A*02:01-restricted epitope of CRNDE 84aa induced a specific human T-cell response. CTLs from a breast cancer patient recognized the CRNDE 84aa epitope (FIMELLYWL) and lysed HLA-A2-positive breast cancer cells expressing CRNDE 84aa. Furthermore, human CD8+ T cells enriched with prioritized cryptic breast cancer antigens protected mice from tumor challenge in autologous PDX models. Conclusions: CRNDE 84aa is highly expressed in breast cancer and functions as a tumor antigen that activates anti-tumor immunity. This study suggests that lncRNA-encoded peptides represent a viable source of tumor antigens for immunologically “cold” tumors such as breast cancer, highlighting their potential as novel targets for immunotherapy.