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. 2022 Aug 6;13:4594. doi: 10.1038/s41467-022-32283-3

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© The Author(s) 2022

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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Fig. 2 — a Expression profiles of canonical marker genes of T/NK subtypes (top) and their tissue preferences (bottom). Dot size indicates the ratios of the observed versus expected cell numbers (R_O/E); Dot color indicates the log-transformed P values determined by two-sided Chi-squared test. T_EM effector memory T, TN Naïve T, T_CM central memory T, Treg regulatory T, NTL non-tumor liver, PT primary tumor, PVTT portal vein tumor thrombus, MLN metastatic lymph node. b Multi-color IHC staining to validate the presence of CD4⁺ T_CM, CD8⁺ T and CD20⁺ B cells aggregates in early tertiary lymphoid structures (E-TLSs) in the tumor of patient HCC03. c Differential abundance of CD4⁺ T_CM (C35) or CD20⁺ B (C40) in TLS^low and TLS^high tumors from TCGA-LIHC cohort estimated using a 9-gene TLS signature. d Higher abundance of CD4⁺ T_CM (C35) or CD20⁺ B (C40) predicts increased overall survival rates of patients in the TCGA-LIHC cohort. e The infiltration rates of T cell subtypes in tumors of HBV-infected (n = 5) and non-HBV/HCV-infected (n = 3) HCC patients, measured by dividing the number of T cells in tumoral tissues with the number of the whole T cell subtype. f The inferred abundances of T cell subtypes in HBV-infected (n = 104), HCV-infected (n = 56) and non-HBV/HCV-infected (n = 216) tumor samples in the TCGA-LIHC cohort. g The k-means clustering of cytotoxic T lymphocytes (CTLs) based on the expression levels of CTLs effector molecules. h Proportions of the exhausted, pre-exhausted and non-exhausted CTLs in HBV-, HCV- or non-HBV/HCV-infected patients. i The differential abundances of exhausted T cells (Tex) and differential expression levels of exhaustion markers in HBV-infected (n = 104), HCV-infected (n = 56) and non-HBV/HCV-infected (n = 216) tumor samples in the TCGA-LIHC cohort. In c, f and i, the statistical significance was determined by two-sided Student’s t test. ns, not significant, *P < 0.05, ^**P < 0.01 and ^***P < 0.001. Boxplot elements are defined in the Methods section (data visualization). Source data are provided as a Source Data file.