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Jia G, He P, Dai T, Goh D, Wang J, Sun M, Wee F, Li F, Lim JCT, Hao S, Liu Y, Lim TKH, Ngo NT, Tao Q, Wang W, Umar A, Nashan B, Zhang Y, Ding C, Yeong J, Liu L, Sun C. Spatial immune scoring system predicts hepatocellular carcinoma recurrence. Nature 2025; 640:1031-1041. [PMID: 40074893 DOI: 10.1038/s41586-025-08668-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 01/17/2025] [Indexed: 03/14/2025]
Abstract
Given the high recurrence rates of hepatocellular carcinoma (HCC) post-resection1-3, improved early identification of patients at high risk for post-resection recurrence would help to improve patient outcomes and prioritize healthcare resources4-6. Here we observed a spatial and HCC recurrence-associated distribution of natural killer (NK) cells in the invasive front and tumour centre from 61 patients. Using extreme gradient boosting and inverse-variance weighting, we developed the tumour immune microenvironment spatial (TIMES) score based on the spatial expression patterns of five biomarkers (SPON2, ZFP36L2, ZFP36, VIM and HLA-DRB1) to predict HCC recurrence risk. The TIMES score (hazard ratio = 88.2, P < 0.001) outperformed current standard tools for patient risk stratification including the TNM and BCLC systems. We validated the model in 231 patients from five multicentred cohorts, achieving a real-world accuracy of 82.2% and specificity of 85.7%. The predictive power of these biomarkers emerged through the integration of their spatial distributions, rather than individual marker expression levels alone. In vivo models, including NK cell-specific Spon2-knockout mice, revealed that SPON2 enhances IFNγ secretion and NK cell infiltration at the invasive front. Our study introduces TIMES, a publicly accessible tool for predicting HCC recurrence risk, offering insights into its potential to inform treatment decisions for early-stage HCC.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Middle Aged
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/surgery
- Cohort Studies
- Extracellular Matrix Proteins/genetics
- Extracellular Matrix Proteins/deficiency
- Extracellular Matrix Proteins/metabolism
- Interferon-gamma/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/cytology
- Liver Neoplasms/diagnosis
- Liver Neoplasms/immunology
- Liver Neoplasms/pathology
- Liver Neoplasms/surgery
- Mice, Knockout
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/pathology
- Reproducibility of Results
- Tumor Microenvironment
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Affiliation(s)
- Gengjie Jia
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiqi He
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Tianli Dai
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Jiabei Wang
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Mengyuan Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Felicia Wee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Fuling Li
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Shuxia Hao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yao Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Tony Kiat Hon Lim
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Duke-NUS Medical School, Singapore, Singapore
| | | | - Qingping Tao
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Wang
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Clinical Research Hospital of Chinese Academy of Sciences, University of Science and Technology of China, Hefei, China
| | - Ahitsham Umar
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Björn Nashan
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China
| | - Yongchang Zhang
- Hunan Cancer Hospital, The Affiliated Cancer Hospital of Central South University, Changsha, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Joe Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Singapore.
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore.
- Cancer Science Institute, National University of Singapore, Singapore, Singapore.
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China.
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), University of Science and Technology of China, Hefei, China.
- Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, Key Laboratory of Immune Response and Immunotherapy, Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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Lau MC, Borowsky J, Väyrynen JP, Haruki K, Zhao M, Dias Costa A, Gu S, da Silva A, Ugai T, Arima K, Nguyen MN, Takashima Y, Yeong J, Tai D, Hamada T, Lennerz JK, Fuchs CS, Wu CJ, Meyerhardt JA, Ogino S, Nowak JA. Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. PLoS Comput Biol 2025; 21:e1012707. [PMID: 39965007 PMCID: PMC11849983 DOI: 10.1371/journal.pcbi.1012707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 02/24/2025] [Accepted: 12/09/2024] [Indexed: 02/20/2025] Open
Abstract
BACKGROUND Growing evidence supports the importance of characterizing the organizational patterns of various cellular constituents in the tumor microenvironment in precision oncology. Most existing data on immune cell infiltrates in tumors, which are based on immune cell counts or nearest neighbor-type analyses, have failed to fully capture the cellular organization and heterogeneity. METHODS We introduce a computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), that jointly measures immune cell partitioning between tumor epithelial and stromal areas and immune cell clustering versus dispersion. As proof-of-principle, we applied TIPC to a prospective cohort incident tumor biobank containing 931 colorectal carcinoma cases. TIPC identified tumor subtypes with unique spatial patterns between tumor cells and T lymphocytes linked to certain molecular pathologic and prognostic features. T lymphocyte identification and phenotyping were achieved using multiplexed (multispectral) immunofluorescence. In a separate hepatocellular carcinoma cohort, we replaced the stromal component with specific immune cell types-CXCR3+CD68+ or CD8+-to profile their spatial relationships with CXCL9+CD68+ cells. RESULTS Six unsupervised TIPC subtypes based on T lymphocyte distribution patterns were identified, comprising two cold and four hot subtypes. Three of the four hot subtypes were associated with significantly longer colorectal cancer (CRC)-specific survival compared to a reference cold subtype. Our analysis showed that variations in T-cell densities among the TIPC subtypes did not strictly correlate with prognostic benefits, underscoring the prognostic significance of immune cell spatial patterns. Additionally, TIPC revealed two spatially distinct and cell density-specific subtypes among microsatellite instability-high colorectal cancers, indicating its potential to upgrade tumor subtyping. TIPC was also applied to additional immune cell types, eosinophils and neutrophils, identified using morphology and supervised machine learning; here two tumor subtypes with similarly low densities, namely 'cold, tumor-rich' and 'cold, stroma-rich', exhibited differential prognostic associations. Lastly, we validated our methods and results using The Cancer Genome Atlas colon and rectal adenocarcinoma data (n = 570). Moreover, applying TIPC to hepatocellular carcinoma cases (n = 27) highlighted critical cell interactions like CXCL9-CXCR3 and CXCL9-CD8. CONCLUSIONS Unsupervised discoveries of microgeometric tissue organizational patterns and novel tumor subtypes using the TIPC algorithm can deepen our understanding of the tumor immune microenvironment and likely inform precision cancer immunotherapy.
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Affiliation(s)
- Mai Chan Lau
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A* STAR), Singapore, Republic of Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A* STAR), Singapore, Republic of Singapore
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jennifer Borowsky
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Juha P. Väyrynen
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Cancer and Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Koichiro Haruki
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Melissa Zhao
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andressa Dias Costa
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Simeng Gu
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annacarolina da Silva
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tomotaka Ugai
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Kota Arima
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Minh N. Nguyen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A* STAR), Singapore, Republic of Singapore
| | - Yasutoshi Takashima
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joe Yeong
- Division of Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency of Science, Technology and Research (A* STAR), Singapore, Republic of Singapore
| | - David Tai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
- Duke NUS Medical School, Singapore, Republic of Singapore
| | - Tsuyoshi Hamada
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jochen K. Lennerz
- BostonGene; Waltham, Boston, Massachusetts, United States of America
| | - Charles S. Fuchs
- Genentech, South San Francisco, California, United States of America
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jeffrey A. Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shuji Ogino
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Harvard Cancer Center, Boston, Massachusetts, United States of America
| | - Jonathan A. Nowak
- Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
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