Fig. 5: Genome-wide screens using TCR-MAP discovers autoantigen reactivities of mouse TCRs.

a, Mouse genome-wide TCR-MAP screen results of the 2C TCR. The 56-aa peptide fragments covering the mouse proteome were expressed in H2-L^d+ G₅-target cells. Each dot in a and e represents one peptide, with the y axis plotting the −log₁₀ adjusted P values determined by Mageck and the x axis calling the geometric mean of the enrichment of the peptide across three replicates. Fold enrichment is defined as the ratio of the abundance of the peptide in the sorted population relative to the input library. b, List of the overlapping fragments that scored in the 2C TCR screen, where the common peptide sequence between the two tiles is underlined. NetMHC was subsequently run to predict three possible 8-aa or 9-aa peptide binders on H2-L^d; these peptides were pulsed on H2-L^d+ G₅-target cells and 2C TCR⁺ SrtA-Jurkat reactivity was assessed. ****P < 0.0001 for each group relative to the no-antigen control, determined by a two-tailed t-test. c, Quantification of H2-L^d+ G₅-target cell biotinylation expressing 56-aa peptide tiles containing the known antigen for OGDH or SLC31A1. d, Table of NetMHC binding affinity predictions for the indicated epitopes from OGDH or SLC31A1 on the H2-L^d allele. e, Mouse genome-wide TCR-MAP screen results of five mouse expanded myocarditis-specific TCRs. H2-K^b/D^b+ G₅-target cells were cultured with multiplexed SrtA-Jurkat cells at an effector-to-target ratio of 1:1. f, Individual TCRs were tested against 56-mer tiles from CKMT2 and RIKEN cDNA. ****P < 0.0001 for each group relative to the no-antigen control for the specific TCR, determined by one-way ANOVA with a Tukey–Kramer multiple-comparison test. g, Predicted H2-K^b or H2-D^b peptide binders were pulsed into G₅-target cells, cocultured with TCR4⁺ SrtA-Jurkats and assessed for biotinylation. h, CKMT2 RPKM (reads per kilobase of transcript per million reads mapped) values from an RNA-seq dataset on 27 human tissues or organs⁴³. Each dot in b, c and g represents a different biological replicate, where error bars indicate the mean and s.d. Data in b, c, e and g are representative of n = 3 independent biological replicates.

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