RNA m6A-Ythdf1 in dendritic cells triggers anti-tumor immunity (RNA-seq and RIP-seq in in GMDCs)

Emerging evidence emphasizes the important role of tumor neoantigen in generating the spontaneous antitumor immune response and predicting the clinical response to immunotherapies. Despite the presence of numerous neoantigens, complete tumor elimination rarely occurs in majority of patients due to failures in mounting a sufficient and lasting antitumor immunity. Here we show that the durable neoanitgen-specific immunity is regulated by a m6A-binding protein, Ythdf1. In contrast to wild-type mice, Ythdf1-deficient (Ythdf1-/-) mice generate more antigen-specific CD8+ T cell response for persistent tumor control. Loss of Ythdf1 in dendritic cell (DC) results in an enhanced cross-presentation of tumor antigen and cross-priming of CD8+ T cell in vivo. To confirm our observations, we performed RNA-Seq to analyze the transcriptional level of genes in DCs and performed RNA Immunoprecipitation (RIP-seq) to locate the binding sites of Ythdf1. To confirm our observations about the functional influence of Ythdf1 on DCs, we performed RNA-Seq to analyze the transcriptional level of genes in DCs from WT and Ythdf1-/- mice. To indentify the mRNA that recognized by Ythdf1, we performed profiling of RNA Immunoprecipitation (RIP-seq) to locate the binding sites of Ythdf1. GMCSF-induced bone marrow DCs (GMDCs) were used for library preparation.