RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) and two control CT26 cell lines (Sun1_Control) using CRISPR-Cas9. By performing RNA-seq on cultured cells, tumors grown in syngeneic model, and purified tumor cells from tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect immune-related pathways and immune cell infiltration and anti-PD1 efficacy in BALB/c mice. Overall design: 1)Sun1_KO and Sun1_Control cells cultured in complete RPMI medium were used for RNA extraction and RNA-seq; 2)Sun1_KO and Sun1_Control cells were subcutaneously injected in the right flank. Tumors were collected at day 14 post-inoculation, and RNA was extracted for RNA-seq; 3)Sun1_KO and Sun1_Control cells were subcutaneously injected in the right flank. Tumors were collected at day 14 post-inoculation, prepared in single cell, and then tumor cells were purified using a mouse tumor cells isolation kit. RNA was extracted from the purified cell lines (Sun1_KO and Sun1_Control) and used for RNA-seq.