Cellular and transcriptional profiles of peripheral blood mononuclear cells pre-vaccination predict immune response to preventative MUC1 vaccine

A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial (NCT02134925) were conducted in individuals with a history of advanced colonic adenoma to test the safety and immunogenicity of the MUC1 tumor antigen vaccine and its potential to prevent new adenomas. These were the first two trials of a non-viral cancer vaccine administered in the absence of cancer. The vaccine was safe and strongly immunogenic in 43% (NCT007773097) and 25% (NCT02134925) of participants. The lack of response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to some level of suppression previously reported only in cancer. Analysis of single-cell RNA-sequencing (scRNA-seq) data from banked pre-vaccination peripheral blood mononuclear cells (PBMCs) (16 immune responders and 16 non-responders) identified specific cell types, genes, and pathways of a productive vaccine response. Responders had a significantly higher percentage of CD4+ naive T cells pre-vaccination, but a significantly lower percentage of CD8+ T effector memory (TEM) cells and CD16+ monocytes. Differential gene expression (DGE) and transcription factor inference analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in CD4+ naive T cells. Pathway analysis showed enriched signaling activity in responders. Furthermore, Bayesian network analyses suggested that these genes were mechanistically related to response. Our analyses identified several immune mechanisms and candidate biomarkers which can be further validated as predictors of immune responses to a preventative cancer vaccine that could facilitate selection of individuals likely to benefit from a vaccine or be used in further research to improve vaccine responses. One Sentence SummarySingle-cell RNA sequencing reveals distinctive cell types, enriched biological pathways, and candidate biomarkers pre-vaccination that predict immune responses to the preventative MUC1 cancer vaccine.