In the present invention, the inventors reveal that noncoding
RNA, a known source of noncanonical peptides (also called dark matter) and tumour-specific antigens, can shape the precancer immune contexture and are associated with polyp and
cancer risk. Through the multimodal characterisation of a unique dataset of 135 well-annotated
cancer and precancer lesions from patients developing polyps at low and
high frequency, the inventors identified high expression of noncoding RNAs, as a major
differentiator of polyp development rate. Noncoding RNAs were also associated with increased
immunogenicity associated with increased mature
tertiary lymphoid structures within the microenvironment of pre-
cancer lesion, higher quantity and quality of adaptive immune cells, including B- and T-cells. Thus, the inventors propose that early
carcinogenesis is shaped by noncoding
RNA expression and
immune microenvironment. These compelling findings reveal potential targets for
immune modulation approaches in individuals at high risk of developing
colorectal cancer. More particularly, the inventors identified dark antigens (i.e. peptides) that can be used in vaccines for the treatment of cancer, in particular, the
prophylactic treatment of cancer.