ResearchIn-Press PreviewImmunologyOncology Open Access | 10.1172/jci.insight.176749
1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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1Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America
2Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
3Department of Research Pathology, Genentech, South San Francisco, United States of America
4Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
5Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States of America
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Published January 14, 2025 - More info
Spatial profiling of tissues promises to elucidate tumor-microenvironment interactions and generate prognostic and predictive biomarkers. We analyzed single-cell, spatial data from three multiplex imaging technologies: cyclic immunofluorescence (CycIF) data we generated from 102 breast cancer patients with clinical follow-up, and publicly available imaging mass cytometry and multiplex ion-beam imaging datasets. Similar single-cell phenotyping results across imaging platforms enabled combined analysis of epithelial phenotypes to delineate prognostic subtypes among estrogen-receptor positive (ER+) patients. We utilized discovery and validation cohorts to identify biomarkers with prognostic value. Increased lymphocyte infiltration was independently associated with longer survival in triple-negative (TN) and high-proliferation ER+ breast tumors. An assessment of ten spatial analysis methods revealed robust spatial biomarkers. In ER+ disease, quiescent stromal cells close to tumor were abundant in good prognosis tumors, while tumor cell neighborhoods containing mixed fibroblast phenotypes were enriched in poor prognosis tumors. In TN disease, macrophage/tumor and B/T lymphocyte neighbors were enriched and lymphocytes were dispersed in good prognosis tumors, while tumor cell neighborhoods containing vimentin-positive fibroblasts were enriched in poor prognosis tumors. In conclusion, we generated comparable single-cell spatial proteomic data from several clinical cohorts to enable prognostic spatial biomarker identification and validation.