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Kürten CHL, Kulkarni A, Cillo AR, Santos PM, Roble AK, Onkar S, Reeder C, Lang S, Chen X, Duvvuri U, Kim S, Liu A, Tabib T, Lafyatis R, Feng J, Gao SJ, Bruno TC, Vignali DAA, Lu X, Bao R, Vujanovic L, Ferris RL. Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing. Nat Commun 2021; 12:7338. [PMID: 34921143 PMCID: PMC8683505 DOI: 10.1038/s41467-021-27619-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/16/2021] [Indexed: 02/08/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the heterogeneity, signatures of unique cell populations, and cell-cell interactions of non-immune and immune cell populations in 6 human papillomavirus (HPV)+ and 12 HPV- HNSCC patient tumor and matched peripheral blood specimens using single-cell RNA sequencing. Using this dataset of 134,606 cells, we show cell type-specific signatures associated with inflammation and HPV status, describe the negative prognostic value of fibroblasts with elastic differentiation specifically in the HPV+ TME, predict therapeutically targetable checkpoint receptor-ligand interactions, and show that tumor-associated macrophages are dominant contributors of PD-L1 and other immune checkpoint ligands in the TME. We present a comprehensive single-cell view of cell-intrinsic mechanisms and cell-cell communication shaping the HNSCC microenvironment.
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Affiliation(s)
- Cornelius H L Kürten
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aditi Kulkarni
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anthony R Cillo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia M Santos
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anna K Roble
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sayali Onkar
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carly Reeder
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephan Lang
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Xueer Chen
- Deparment of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Seungwon Kim
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Angen Liu
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jian Feng
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Shou-Jiang Gao
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tullia C Bruno
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dario A A Vignali
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinghua Lu
- Deparment of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Riyue Bao
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lazar Vujanovic
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert L Ferris
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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