Figure 6

Viral memory T cell detection in a cervical patient blood sample. (A) 30 × 10⁶ PBMCs from an HLA-A*02:01⁺ patient with early-stage, treatment-naïve cervical cancer were tested in an IFNγ ELISPOT assay for reactivity against a panel of human papilloma virus (HPV16) E6 15-mer synthetic long peptides (SLP) and 5 HLA-A*02:01-restricted CEF 9-mer peptides. The number of IFNγ spots per 2 × 10⁵ PBMC is shown. (B) Unexpanded PBMC (7 × 10⁶ PBMC per assay well) from the patient in (A) were tested in RAPTER to identify HPV16 E6 and CEF peptide specific CD8⁺ T cells. UMAP of total sorted CD8⁺ T cells and CD137/4-1BB⁺ T cells from the RAPTER assay. (C) RAPTER signal was demultiplexed by HTO labels to assign individual T cells with cognate peptide reactivities. Out of a total of 3,129T cells, 352 unique TCR clones were identified. TCR clone size (y-axis) is plotted for each HTO designation (x-axis). (D) TCR clones identified by RAPTER to be specific for HPV and CEF epitopes are projected onto the scRNA-SEQ UMAP from panel (B). The color scale represents the TCR clone size. (E) Heat map showing top 16 differentially expressed genes among the Influenza M, HPV16_E6_101, EBV BMLF1, and LMP2A reactive T cell clusters from (D).