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Nyman J, Denize T, Bakouny Z, Labaki C, Titchen BM, Bi K, Hari SN, Rosenthal J, Mehta N, Jiang B, Sharma B, Felt K, Umeton R, Braun DA, Rodig S, Choueiri TK, Signoretti S, Van Allen EM. Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. Cell Rep Med 2023; 4:101189. [PMID: 37729872 PMCID: PMC10518628 DOI: 10.1016/j.xcrm.2023.101189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is molecularly heterogeneous, immune infiltrated, and selectively sensitive to immune checkpoint inhibition (ICI). However, the joint tumor-immune states that mediate ICI response remain elusive. We develop spatially aware deep-learning models of tumor and immune features to learn representations of ccRCC tumors using diagnostic whole-slide images (WSIs) in untreated and treated contexts (n = 1,102 patients). We identify patterns of grade heterogeneity in WSIs not achievable through human pathologist analysis, and these graph-based "microheterogeneity" structures associate with PBRM1 loss of function and with patient outcomes. Joint analysis of tumor phenotypes and immune infiltration identifies a subpopulation of highly infiltrated, microheterogeneous tumors responsive to ICI. In paired multiplex immunofluorescence images of ccRCC, microheterogeneity associates with greater PD1 activation in CD8+ lymphocytes and increased tumor-immune interactions. Our work reveals spatially interacting tumor-immune structures underlying ccRCC biology that may also inform selective response to ICI.
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Affiliation(s)
- Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Graduate Program in Systems Biology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Breanna M Titchen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Surya Narayanan Hari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Jacob Rosenthal
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicita Mehta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bowen Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Stanford University, Stanford, CA, USA
| | - Bijaya Sharma
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen Felt
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renato Umeton
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David A Braun
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Sabina Signoretti
- Broad Institute, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
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Nyman J, Denize T, Bakouny Z, Labaki C, Titchen BM, Bi K, Hari SN, Rosenthal J, Mehta N, Jiang B, Sharma B, Felt K, Umeton R, Braun DA, Rodig S, Choueiri TK, Signoretti S, Van Allen EM. Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524545. [PMID: 36712053 PMCID: PMC9882334 DOI: 10.1101/2023.01.18.524545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is molecularly heterogeneous, immune infiltrated, and selectively sensitive to immune checkpoint inhibition (ICI). Established histopathology paradigms like nuclear grade have baseline prognostic relevance for ccRCC, although whether existing or novel histologic features encode additional heterogeneous biological and clinical states in ccRCC is uncertain. Here, we developed spatially aware deep learning models of tumor- and immune-related features to learn representations of ccRCC tumors using diagnostic whole-slide images (WSI) in untreated and treated contexts (n = 1102 patients). We discovered patterns of nuclear grade heterogeneity in WSI not achievable through human pathologist analysis, and these graph-based "microheterogeneity" structures associated with PBRM1 loss of function, adverse clinical factors, and selective patient response to ICI. Joint computer vision analysis of tumor phenotypes with inferred tumor infiltrating lymphocyte density identified a further subpopulation of highly infiltrated, microheterogeneous tumors responsive to ICI. In paired multiplex immunofluorescence images of ccRCC, microheterogeneity associated with greater PD1 activation in CD8+ lymphocytes and increased tumor-immune interactions. Thus, our work reveals novel spatially interacting tumor-immune structures underlying ccRCC biology that can also inform selective response to ICI.
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Affiliation(s)
- Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Graduate Program in Systems Biology, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Breanna M Titchen
- Harvard Graduate Program in Biological and Biomedical Sciences, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Surya Narayanan Hari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Jacob Rosenthal
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicita Mehta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bowen Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Stanford University, Stanford, CA, USA
| | - Bijaya Sharma
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Kristen Felt
- ImmunoProfile, Department of Pathology, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Renato Umeton
- Department of Informatics & Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David A Braun
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Sabina Signoretti
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
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