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. 2021 Jul 21;596(7870):126–132. doi: 10.1038/s41586-021-03752-4

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© The Author(s) 2021, corrected publication 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 11 — The canonical correlation between pathologic response status and CD8 T cell clusters vs. a MANA-specific T cell-enriched cluster was evaluated. a, Selection of MANA-specific T cell enriched clusters (Proliferating, TRM(IV), TRM (V) and TRM (II)) based on >2 fold change (red dotted line) of MANA-specific T cell frequency relative to random expectation. The above 4 clusters were combined as a ‘MANA-combined’ cluster. b, Combined MANA-specific T cell enriched clusters showed the highest canonical correlation with pathologic response. c, PCA of pseudobulk gene expression from all CD8 T cell clusters for individual tumour samples (n = 15, 6 MPRs and 9 non-MPRs), coloured by response status (MPR as blue blue dots, non-MPR as red dots). d, PCA of pseudobulk gene expression from combined MANA enriched T cell cluster for individual tumour samples (n = 15, 6 MPRs and 9 non-MPRs), coloured by response status (MPR as light blue dots, non-MPR as red dots). P values were obtained using a one-sided permutation test, without correction for multiple comparisons.