Fig. 3

SMG1 expression affects the TCR repertoire and conditions PTC-neoantigen immune responses. (A) Panc02 or 4T1 (gCtrl or SMG1^KD) tumor-bearing mice are sacrificed on day 14 post-inoculation and tumor draining lymph node mRNA is isolated for TCRseq. Abundance of the TRBV segment present in the most frequent clones (>50 copies) was analyzed. n = 3/group (Panc02.SMG1^KD); n = 3/group (Panc02.gCtrl); n = 3/group (4T1.SMG1^KD); n = 2/group (4T1.gCtrl). (B) K-means t-sne clustering of TRBV segment from (A). n = 3/group (Panc02.SMG1KD); n = 3/group (Panc02.gCtrl); n = 3/group (4T1.SMG1^KD); n = 2/group (4T1.gCtrl). (C) Pipeline followed for neoantigen discovery in 4T1 mouse breast model. (D) Integrated Genome Browser (IGV) view of the +1 insertion in Trp53 present in 4T1 cells. (E) ELISPOT determining NMD-controlled immune response induction of p53 neoantigen in 4T1 tumor-bearing mice. Balb/c mice were sacrificed on day 14 post-inoculation of gCtrl or SMG1^KD 4T1 tumors and draining lymph nodes were isolated. Obtained cells were co-cultured with the candidate peptides to test antigen recognition. n = 10/group. (F) Proportion of responding and non-responding mice to Trp53 neoantigen in (E). All SMG1^KD tumor-bearing mice show response to Trp53 peptide compared to the 50% of gCtrl group