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Ray A, Bassette M, Hu KH, Pass LF, Samad B, Combes A, Johri V, Davidson B, Hernandez G, Zaleta-Linares I, Krummel MF. Multimodal identification of rare potent effector CD8 T cells in solid tumors. bioRxiv 2023:2023.09.26.559470. [PMID: 37808790 PMCID: PMC10557647 DOI: 10.1101/2023.09.26.559470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Antitumor immunity is driven by CD8 T cells, yet we lack signatures for the exceptional effectors in tumors, amongst the vast majority of CD8 T cells undergoing exhaustion. By leveraging the measurement of a canonical T cell activation protein (CD69) together with its RNA (Cd69), we found a larger classifier for TCR stimulation-driven effector states in vitro and in vivo. This revealed exceptional 'star' effectors-highly functional cells distinguished amidst progenitor and terminally exhausted cells. Although rare in growing mouse and human tumors, they are prominent in mice during T cell-mediated tumor clearance, where they engage with tumor antigen and are superior in tumor cell killing. Employing multimodal CITE-Seq allowed de novo identification of similar rare effectors amidst T cell populations in human cancer. The identification of rare and exceptional immune states provides rational avenues for enhancement of antitumor immunity.
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Affiliation(s)
- Arja Ray
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
| | - Molly Bassette
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
| | - Kenneth H Hu
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
| | - Lomax F Pass
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
| | - Bushra Samad
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
- UCSF CoLabs, University of California, San Francisco, CA 94143, USA
| | - Alexis Combes
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
- UCSF CoLabs, University of California, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Vrinda Johri
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
- UCSF CoLabs, University of California, San Francisco, CA 94143, USA
| | - Brittany Davidson
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
- UCSF CoLabs, University of California, San Francisco, CA 94143, USA
| | - Grace Hernandez
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Itzia Zaleta-Linares
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, CA 94143, USA
- ImmunoX Initiative, University of California, San Francisco, CA 94143, USA
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Rahim MK, Okholm TLH, Jones KB, McCarthy EE, Liu CC, Yee JL, Tamaki SJ, Marquez DM, Tenvooren I, Wai K, Cheung A, Davidson BR, Johri V, Samad B, O'Gorman WE, Krummel MF, van Zante A, Combes AJ, Angelo M, Fong L, Algazi AP, Ha P, Spitzer MH. Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes. Cell 2023; 186:1127-1143.e18. [PMID: 36931243 PMCID: PMC10348701 DOI: 10.1016/j.cell.2023.02.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment, recent studies in mice identified responses in lymph nodes (LNs) as essential; however, the role of LNs in human cancer patients remains unknown. We examined CD8+ T cells in human head and neck squamous cell carcinomas, regional LNs, and blood using mass cytometry, single-cell genomics, and multiplexed ion beam imaging. We identified progenitor exhausted CD8+ T cells (Tpex) that were abundant in uninvolved LN and clonally related to terminally exhausted cells in the tumor. After anti-PD-L1 immunotherapy, Tpex in uninvolved LNs reduced in frequency but localized near dendritic cells and proliferating intermediate-exhausted CD8+ T cells (Tex-int), consistent with activation and differentiation. LN responses coincided with increased circulating Tex-int. In metastatic LNs, these response hallmarks were impaired, with immunosuppressive cellular niches. Our results identify important roles for LNs in anti-tumor immune responses in humans.
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Affiliation(s)
- Maha K Rahim
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trine Line H Okholm
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kyle B Jones
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Pharma Technical Cell and Gene Therapy, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Elizabeth E McCarthy
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Candace C Liu
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | - Jacqueline L Yee
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stanley J Tamaki
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diana M Marquez
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Iliana Tenvooren
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine Wai
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Cheung
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brittany R Davidson
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vrinda Johri
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bushra Samad
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - William E O'Gorman
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Matthew F Krummel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Annemieke van Zante
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Alain P Algazi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Ha
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew H Spitzer
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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