Fig. 3: MANAscore can identify putative tumor-reactive TIL. | Nature Communications

Fig. 3: MANAscore can identify putative tumor-reactive TIL.

From: A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types

Fig. 3

A Cell overlays to show the UMAP localization of functionally validated MANA-specific TIL, functionally validated MANAscorehi MANA-specific TIL, all pTRC (n = 45,190), and MANAscorehi pTRC (n = 17,382) on the CD8+ UMAP. B Functionally validated tumor-reactive TIL (n = 136 cells) overlaid on the CD8+ TIL UMAP of the Luoma et al. oral cancer cohort (top left) and the overall MANAscore (\(\sqrt{{{{\rm{MANAscore}}}\_{{\rm{i}}}}^{2}+{{{\rm{MANAscore}}}\_{{\rm{ni}}}}^{2}}\)) predicted for CD8+ TIL in the same cohort (top right). Functionally validated MANA-specific TIL (n = 303 cells) overlaid on the CD8+ TIL UMAP of the Lowery et al. metastatic cancer cohort (bottom left) and the overall MANAscore (\(\sqrt{{{{\rm{MANAscore}}}\_{{\rm{i}}}}^{2}+{{{\rm{MANAscore}}}\_{{\rm{ni}}}}^{2}}\)) overlaid on the same UMAP (bottom right) is also shown. MANAscore ranges from 0 (blue) to 1 (red). C UMAP projection of the expression profiles of 43,880 CD8+ T cells from three Merkel cell carcinoma patients with MCPyV-positive. Immune cell subsets, defined by 9 unique clusters, are annotated and marked by color code. D CITEseq identified MCPyV-specific TIL of high quality (n = 4473 cells) overlaid on the CD8+ TIL UMAP of Merkel cell carcinoma cohort from patients with MCPyV positive. E Overall MANAscore (\(\sqrt{{{{\rm{MANAscore}}}\_{{\rm{i}}}}^{2}+{{{\rm{MANAscore}}}\_{{\rm{ni}}}}^{2}}\)) predicted for CD8+ TIL in the same cohort (right). F Scatter plot of MANAscore_i and MANAscore_ni for TIL in three Merkel cell carcinoma patient. The TIL captured by both CITEseq and MANAscore were marked red (n = 4466 in total), the TIL only captured by CITEseq were marked green (n = 7). The linear correlation of these two scores was marked in green, Pearson’s correlation coefficient is added. G pTRC and MANAscorehi pTRC identified overlayed on the CD8+ UMAP of Merkel cell carcinoma. H Venn diagram of TIL identified by MANAscore (pTRC, n = 8640) and CITEseq (MCPyV-specific TIL, n = 4473), of which 4401 (99.05%) TIL were identified by both methods.

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