Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

• Mai Chan Lau ,

  Roles Conceptualization, Formal analysis, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  ¶☯ Contributed equally as co-first authors.

  Affiliations 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

  https://orcid.org/0000-0002-7698-4697

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• Jennifer Borowsky ,

  Roles Data curation, Methodology, Writing – original draft

  ¶☯ Contributed equally as co-first authors.

  Affiliation Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia

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• Juha P. Väyrynen ,

  Roles Data curation, Investigation, Methodology, Validation, Writing – original draft, Writing – review & editing

  ¶☯ Contributed equally as co-first authors.

  Affiliations 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

  https://orcid.org/0000-0002-8683-2996

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• Koichiro Haruki ,

  Roles Data curation, Investigation, Writing – original draft, Writing – review & editing

  ¶☯ Contributed equally as co-first authors.

  Affiliations 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

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• Melissa Zhao,

  Roles Investigation

  Affiliation Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Andressa Dias Costa,

  Roles Data curation, Visualization

  Affiliation Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America

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• Simeng Gu,

  Roles Formal analysis

  Affiliation Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Annacarolina da Silva,

  Roles Data curation, Visualization

  Affiliation Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Tomotaka Ugai,

  Roles Data curation, Visualization

  Affiliations 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

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• Kota Arima,

  Roles Data curation, Visualization

  Affiliation Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Minh N. Nguyen,

  Roles Software

  Affiliation Bioinformatics Institute (BII), Agency for Science, Technology and Research (A* STAR), Singapore, Republic of Singapore

  https://orcid.org/0000-0003-4949-2571

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• Yasutoshi Takashima,

  Roles Data curation, Visualization

  Affiliations 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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• Joe Yeong,

  Roles Data curation, Writing – original draft

  Affiliations 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

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• David Tai,

  Roles Data curation, Writing – original draft

  Affiliations Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore, Duke NUS Medical School, Singapore, Republic of Singapore

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• Tsuyoshi Hamada,

  Roles Data curation

  Affiliation Department of Pathology, Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Jochen K. Lennerz,

  Roles Writing – review & editing

  Affiliation BostonGene; Waltham, Boston, Massachusetts, United States of America

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• Charles S. Fuchs,

  Roles Funding acquisition, Writing – review & editing

  Affiliation Genentech, South San Francisco, California, United States of America

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• Catherine J. Wu,

  Roles Writing – review & editing

  Affiliations 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

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• Jeffrey A. Meyerhardt,

  Roles Writing – review & editing

  Affiliation Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America

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• Shuji Ogino ,

  Roles Conceptualization, Data curation, Funding acquisition, Methodology, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: sogino@bwh.harvard.edu (SO); janowak@bwh.harvard.edu (JAN)

  ¶‡ SO and JAN Contributed equally as co-last authors.

  Affiliations 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

  https://orcid.org/0000-0002-3909-2323

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•  [ ... ],
• Jonathan A. Nowak

  Roles Conceptualization, Funding acquisition, Methodology, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: sogino@bwh.harvard.edu (SO); janowak@bwh.harvard.edu (JAN)

  ¶‡ SO and JAN Contributed equally as co-last authors.

  Affiliations 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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