Extended Data Fig. 1. Confirming the presence of bacteria in tumor tissues (see also Fig. 1, Extended Data Fig. 2 and Supplementary Table 4).

a, HLA-II immunopeptidome analyses for bacterial peptides in control including brain lesions of 3 MS patients and brain tissue of 6 healthy donors. A total of 55 bacterial peptides was identified from all the samples. Identical bacterial peptides in the control cohort were removed from the GBM tumor-specific bacterial peptides. b, 16S rRNA gene sequencing confirmed bacteria in tumor tissues of 10 GBM patients, from whom immunopeptidome analyses were available. OTUs relative abundance in read counts were shown at the phylum level for each tumor (Supplementary Tables 5 and 6). * 16S rRNA data from patient 1635WI includes both primary and recurrent tumors of the patient in triplicates. OTUs relative abundance was calculated based on mean OTU of the triplicates divided by total OTUs in each tumor. c, Deduced core binding motif all HLA-DR-derived peptides annotated to human/tumor proteins and UniProt bacterial peptides from primary and recurrent tumors (patient 1635WI) were compared using iceLogo (p = 0.05, two-tailed independent t-test by IceLogo⁵⁸). Light blue squares show the known anchor positions for corresponding HLA-DR molecules⁶².