1
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Krakow EF, Brault M, Summers C, Cunningham TM, Biernacki MA, Black RG, Woodward KB, Vartanian N, Kanaan SB, Yeh AC, Dossa RG, Bar M, Cassaday RD, Dahlberg A, Till BG, Denker AE, Yeung CCS, Gooley TA, Maloney DG, Riddell SR, Greenberg PD, Chapuis AG, Newell EW, Furlan SN, Bleakley M. HA-1-targeted T cell receptor (TCR) T cell therapy for recurrent leukemia after hematopoietic stem cell transplantation. Blood 2024:blood.2024024105. [PMID: 38683966 DOI: 10.1182/blood.2024024105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Relapse is the leading cause of death after allogeneic hematopoietic stem cell transplantation (HCT) for leukemia. T cells engineered by gene transfer to express T cell receptors (TCR; TCR-T) specific for hematopoietic-restricted minor histocompatibility (H) antigens may provide a potent selective anti-leukemic effect post-HCT. We conducted a phase I clinical trial employing a novel TCR-T product targeting the minor H antigen HA-1 to treat or consolidate treatment of persistent or recurrent leukemia and myeloid neoplasms. The primary objective was to evaluate the feasibility and safety of administration of HA-1 TCR-T post-HCT. CD8+ and CD4+ T cells expressing the HA-1 TCR and a CD8-co-receptor were successfully manufactured from HA-1 disparate HCT donors. One or more infusions of HA-1 TCR-T following lymphodepleting chemotherapy were administered to nine HCT recipients who had developed disease recurrence post-HCT. TCR-T cells expanded and persisted in vivo after adoptive transfer. No dose-limiting toxicities occurred. Although the study was not designed to assess efficacy, four patients achieved or maintained complete remissions following lymphodepletion and HA-1 TCR-T, with one ongoing at >2 years. Single-cell RNA sequencing of relapsing/progressive leukemia after TCR-T therapy identified upregulated molecules associated with T cell dysfunction or cancer cell survival. HA-1 TCR-T therapy appears feasible and safe and shows preliminary signals of efficacy. This clinical trial is registered at clinicaltrials.gov as NCT03326921.
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Affiliation(s)
| | | | - Corinne Summers
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Tanya M Cunningham
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | | | - R Graeme Black
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | | | - Nicole Vartanian
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | - Sami B Kanaan
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Albert C Yeh
- University of Washington School of Medicine, United States
| | - Robson G Dossa
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Merav Bar
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Ryan D Cassaday
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | - Ann Dahlberg
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | - Brian G Till
- University of Washington School of Medicine, United States
| | | | | | - Ted A Gooley
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | | | | | | | - Aude G Chapuis
- University of Washington School of Medicine, United States
| | - Evan W Newell
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Scott N Furlan
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Marie Bleakley
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
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2
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Glass DR, Mayer-Blackwell K, Ramchurren N, Parks KR, Duran GE, Wright AK, Bastidas Torres AN, Islas L, Kim YH, Fling SP, Khodadoust MS, Newell EW. Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma. Cell Rep Med 2024:101527. [PMID: 38670099 DOI: 10.1016/j.xcrm.2024.101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/17/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been systematically characterized. We apply a suite of high-dimensional technologies to investigate the local, cellular, and systemic responses in CTCL patients receiving either mono- or combination anti-PD-1 plus interferon-gamma (IFN-γ) therapy. Neoplastic T cells display no evidence of activation after immunotherapy. IFN-γ induces muted endogenous immunological responses, while anti-PD-1 elicits broader changes, including increased abundance of CLA+CD39+ T cells. We develop an unbiased multi-omic profiling approach enabling discovery of immune modules stratifying patients. We identify an enrichment of activated regulatory CLA+CD39+ T cells in non-responders and activated cytotoxic CLA+CD39+ T cells in leukemic patients. Our results provide insights into the effects of immunotherapy in CTCL patients and a generalizable framework for multi-omic analysis of clinical trials.
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Affiliation(s)
- David R Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - George E Duran
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Wright
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Youn H Kim
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven P Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael S Khodadoust
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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3
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Lum FM, Chan YH, Teo TH, Becht E, Amrun SN, Teng KW, Hartimath SV, Yeo NK, Yee WX, Ang N, Torres-Ruesta AM, Fong SW, Goggi JL, Newell EW, Renia L, Carissimo G, Ng LF. Crosstalk between CD64 +MHCII + macrophages and CD4 + T cells drives joint pathology during chikungunya. EMBO Mol Med 2024; 16:641-663. [PMID: 38332201 PMCID: PMC10940729 DOI: 10.1038/s44321-024-00028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/26/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Communications between immune cells are essential to ensure appropriate coordination of their activities. Here, we observed the infiltration of activated macrophages into the joint-footpads of chikungunya virus (CHIKV)-infected animals. Large numbers of CD64+MHCII+ and CD64+MHCII- macrophages were present in the joint-footpad, preceded by the recruitment of their CD11b+Ly6C+ inflammatory monocyte precursors. Recruitment and differentiation of these myeloid subsets were dependent on CD4+ T cells and GM-CSF. Transcriptomic and gene ontology analyses of CD64+MHCII+ and CD64+MHCII- macrophages revealed 89 differentially expressed genes, including genes involved in T cell proliferation and differentiation pathways. Depletion of phagocytes, including CD64+MHCII+ macrophages, from CHIKV-infected mice reduced disease pathology, demonstrating that these cells play a pro-inflammatory role in CHIKV infection. Together, these results highlight the synergistic dynamics of immune cell crosstalk in driving CHIKV immunopathogenesis. This study provides new insights in the disease mechanism and offers opportunities for development of novel anti-CHIKV therapeutics.
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Affiliation(s)
- Fok-Moon Lum
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore.
| | - Yi-Hao Chan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Teck-Hui Teo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Etienne Becht
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Karen Ww Teng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Siddesh V Hartimath
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Nicholas Kw Yeo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Wearn-Xin Yee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Nicholas Ang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Anthony M Torres-Ruesta
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Julian L Goggi
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Lisa Fp Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research, Singapore, 138648, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZX, UK.
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4
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Barboy O, Bercovich A, Li H, Eyal-Lubling Y, Yalin A, Shapir Itai Y, Abadie K, Zada M, David E, Shlomi-Loubaton S, Katzenelenbogen Y, Jaitin DA, Gur C, Yofe I, Feferman T, Cohen M, Dahan R, Newell EW, Lifshitz A, Tanay A, Amit I. Modeling T cell temporal response to cancer immunotherapy rationalizes development of combinatorial treatment protocols. Nat Cancer 2024:10.1038/s43018-024-00734-z. [PMID: 38429414 DOI: 10.1038/s43018-024-00734-z] [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] [Received: 09/03/2023] [Accepted: 01/19/2024] [Indexed: 03/03/2024]
Abstract
Successful immunotherapy relies on triggering complex responses involving T cell dynamics in tumors and the periphery. Characterizing these responses remains challenging using static human single-cell atlases or mouse models. To address this, we developed a framework for in vivo tracking of tumor-specific CD8+ T cells over time and at single-cell resolution. Our tools facilitate the modeling of gene program dynamics in the tumor microenvironment (TME) and the tumor-draining lymph node (tdLN). Using this approach, we characterize two modes of anti-programmed cell death protein 1 (PD-1) activity, decoupling induced differentiation of tumor-specific activated precursor cells from conventional type 1 dendritic cell (cDC1)-dependent proliferation and recruitment to the TME. We demonstrate that combining anti-PD-1 therapy with anti-4-1BB agonist enhances the recruitment and proliferation of activated precursors, resulting in tumor control. These data suggest that effective response to anti-PD-1 therapy is dependent on sufficient influx of activated precursor CD8+ cells to the TME and highlight the importance of understanding system-level dynamics in optimizing immunotherapies.
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Affiliation(s)
- Oren Barboy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hanjie Li
- Department of Synthetic Immunology, Shenzhen Institutes of Advanced Technology, Shenzhen, China
| | - Yaniv Eyal-Lubling
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Adam Yalin
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Shapir Itai
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Kathleen Abadie
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Mor Zada
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Shlomi-Loubaton
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Diego Adhemar Jaitin
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chamutal Gur
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- The Hebrew University, Jerusalem, Israel
| | - Ido Yofe
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Feferman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Cohen
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rony Dahan
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Evan W Newell
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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5
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Pulliam T, Jani S, Jing L, Ryu H, Jojic A, Shasha C, Zhang J, Kulikauskas R, Church C, Garnett-Benson C, Gooley T, Chapuis A, Paulson K, Smith KN, Pardoll DM, Newell EW, Koelle DM, Topalian SL, Nghiem P. Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101412. [PMID: 38340723 PMCID: PMC10897614 DOI: 10.1016/j.xcrm.2024.101412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Understanding cancer immunobiology has been hampered by difficulty identifying cancer-specific T cells. Merkel cell polyomavirus (MCPyV) causes most Merkel cell carcinomas (MCCs). All patients with virus-driven MCC express MCPyV oncoproteins, facilitating identification of virus (cancer)-specific T cells. We studied MCPyV-specific T cells from 27 patients with MCC using MCPyV peptide-HLA-I multimers, 26-color flow cytometry, single-cell transcriptomics, and T cell receptor (TCR) sequencing. In a prospective clinical trial, higher circulating MCPyV-specific CD8 T cell frequency before anti-PD-1 treatment was strongly associated with 2-year recurrence-free survival (75% if detectable, 0% if undetectable, p = 0.0018; ClinicalTrial.gov: NCT02488759). Intratumorally, such T cells were typically present, but their frequency did not significantly associate with response. Circulating MCPyV-specific CD8 T cells had increased stem/memory and decreased exhaustion signatures relative to their intratumoral counterparts. These results suggest that cancer-specific CD8 T cells in the blood may play a role in anti-PD-1 responses. Thus, strategies that augment their number or mobilize them into tumors could improve outcomes.
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Affiliation(s)
- Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saumya Jani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ana Jojic
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn Shasha
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jiajia Zhang
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rima Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aude Chapuis
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Paulson
- Paul G. Allen Research Center, Providence-Swedish Cancer Institute, Seattle, WA 98104, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kellie N Smith
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Suzanne L Topalian
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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6
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Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, Newell EW. Merkel cell polyomavirus-specific and CD39 +CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101390. [PMID: 38340724 PMCID: PMC10897544 DOI: 10.1016/j.xcrm.2023.101390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39+CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells.
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Affiliation(s)
- Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Korok Sarkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Candice D Church
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Nandita Kumar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Saumya Jani
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulla K Hansen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steven P Fling
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA.
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7
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Portuguese AJ, Fang M, Tuazon SA, Pont M, Qu X, Shasha C, Comstock M, Lyons J, Cole G, Newell EW, Glynn E, Soma LA, Green DJ. Acquired CD38 gene deletion as a mechanism of tumor antigen escape in multiple myeloma. Blood Adv 2023; 7:7235-7238. [PMID: 37844282 PMCID: PMC10698540 DOI: 10.1182/bloodadvances.2023011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Affiliation(s)
- Andrew J. Portuguese
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- University of Washington, Department of Medicine, Seattle, WA
| | - Min Fang
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- University of Washington, Department of Medicine, Seattle, WA
| | - Sherilyn A. Tuazon
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- Bristol Myers Squibb, Seattle, WA
| | - Margot Pont
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- CellPoint Bio, a Galapagos company, Oegstgeest, The Netherlands
| | - Xiaoyu Qu
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- University of Washington, Department of Medicine, Seattle, WA
| | - Carolyn Shasha
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
| | - Melissa Comstock
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
| | - Justina Lyons
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
| | - Gabriel Cole
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- CellPoint Bio, a Galapagos company, Oegstgeest, The Netherlands
| | - Evan W. Newell
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- University of Washington, Department of Medicine, Seattle, WA
| | - Emily Glynn
- University of Washington, Department of Medicine, Seattle, WA
| | - Lorinda A. Soma
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- City of Hope Medical Center, Department of Pathology, Duarte, CA
| | - Damian J. Green
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, WA
- University of Washington, Department of Medicine, Seattle, WA
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8
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Schmidt F, Fields HF, Purwanti Y, Milojkovic A, Salim S, Wu KX, Simoni Y, Vitiello A, MacLeod DT, Nardin A, Newell EW, Fink K, Wilm A, Fehlings M. In-depth analysis of human virus-specific CD8 + T cells delineates unique phenotypic signatures for T cell specificity prediction. Cell Rep 2023; 42:113250. [PMID: 37837618 DOI: 10.1016/j.celrep.2023.113250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
Following viral infection, the human immune system generates CD8+ T cell responses to virus antigens that differ in specificity, abundance, and phenotype. A characterization of virus-specific T cell responses allows one to assess infection history and to understand its contribution to protective immunity. Here, we perform in-depth profiling of CD8+ T cells binding to CMV-, EBV-, influenza-, and SARS-CoV-2-derived antigens in peripheral blood samples from 114 healthy donors and 55 cancer patients using high-dimensional mass cytometry and single-cell RNA sequencing. We analyze over 500 antigen-specific T cell responses across six different HLA alleles and observed unique phenotypes of T cells specific for antigens from different virus categories. Using machine learning, we extract phenotypic signatures of antigen-specific T cells, predict virus specificity for bulk CD8+ T cells, and validate these predictions, suggesting that machine learning can be used to accurately predict antigen specificity from T cell phenotypes.
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Affiliation(s)
| | | | | | | | | | - Kan Xing Wu
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | | | | | | | | | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katja Fink
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | - Andreas Wilm
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
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9
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Mayer-Blackwell K, Ryu H, Codd AS, Parks KR, MacMillan HR, Cohen KW, Stewart TL, Seese A, Lemos MP, De Rosa SC, Czartoski JL, Moodie Z, Nguyen LT, McGuire DJ, Ahmed R, Fiore-Gartland A, McElrath MJ, Newell EW. mRNA vaccination boosts S-specific T cell memory and promotes expansion of CD45RA int T EMRA-like CD8 + T cells in COVID-19 recovered individuals. Cell Rep Med 2023; 4:101149. [PMID: 37552991 PMCID: PMC10439252 DOI: 10.1016/j.xcrm.2023.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/30/2023] [Revised: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
SARS-CoV-2 infection and mRNA vaccination both elicit spike (S)-specific T cell responses. To analyze how T cell memory from prior infection influences T cell responses to vaccination, we evaluated functional T cell responses in naive and previously infected vaccine recipients. Pre-vaccine S-specific responses are predictive of subsequent CD8+ T cell vaccine-response magnitudes. Comparing baseline with post-vaccination TCRβ repertoires, we observed large clonotypic expansions correlated with the frequency of spike-specific T cells. Epitope mapping the largest CD8+ T cell responses confirms that an HLA-A∗03:01 epitope was highly immunodominant. Peptide-MHC tetramer staining together with mass cytometry and single-cell sequencing permit detailed phenotyping and clonotypic tracking of these S-specific CD8+ T cells. Our results demonstrate that infection-induced S-specific CD8+ T cell memory plays a significant role in shaping the magnitude and clonal composition of the circulating T cell repertoire after vaccination, with mRNA vaccination promoting CD8+ memory T cells to a TEMRA-like phenotype.
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Amy S Codd
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh R MacMillan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Terri L Stewart
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Maria P Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Long T Nguyen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Donald J McGuire
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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10
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Evrard M, Becht E, Fonseca R, Obers A, Park SL, Ghabdan-Zanluqui N, Schroeder J, Christo SN, Schienstock D, Lai J, Burn TN, Clatch A, House IG, Beavis P, Kallies A, Ginhoux F, Mueller SN, Gottardo R, Newell EW, Mackay LK. Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts. Immunity 2023:S1074-7613(23)00262-5. [PMID: 37392736 DOI: 10.1016/j.immuni.2023.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/08/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Memory CD8+ T cells can be broadly divided into circulating (TCIRCM) and tissue-resident memory T (TRM) populations. Despite well-defined migratory and transcriptional differences, the phenotypic and functional delineation of TCIRCM and TRM cells, particularly across tissues, remains elusive. Here, we utilized an antibody screening platform and machine learning prediction pipeline (InfinityFlow) to profile >200 proteins in TCIRCM and TRM cells in solid organs and barrier locations. High-dimensional analyses revealed unappreciated heterogeneity within TCIRCM and TRM cell lineages across nine different organs after either local or systemic murine infection models. Additionally, we demonstrated the relative effectiveness of strategies allowing for the selective ablation of TCIRCM or TRM populations across organs and identified CD55, KLRG1, CXCR6, and CD38 as stable markers for characterizing memory T cell function during inflammation. Together, these data and analytical framework provide an in-depth resource for memory T cell classification in both steady-state and inflammatory conditions.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
| | - Etienne Becht
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Simone L Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Nagela Ghabdan-Zanluqui
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Jan Schroeder
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Susan N Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Dominik Schienstock
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Junyun Lai
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Thomas N Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Imran G House
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Paul Beavis
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Scott N Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre Hospitalier Universitaire du Vaud and University of Lausanne, Lausanne 1011, Switzerland
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
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11
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Jones DC, Danaher P, Kim Y, Beechem JM, Gottardo R, Newell EW. An information theoretic approach to detecting spatially varying genes. Cell Rep Methods 2023; 3:100507. [PMID: 37426750 PMCID: PMC10326450 DOI: 10.1016/j.crmeth.2023.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023]
Abstract
A key step in spatial transcriptomics is identifying genes with spatially varying expression patterns. We adopt an information theoretic perspective to this problem by equating the degree of spatial coherence with the Jensen-Shannon divergence between pairs of nearby cells and pairs of distant cells. To avoid the notoriously difficult problem of estimating information theoretic divergences, we use modern approximation techniques to implement a computationally efficient algorithm designed to scale with in situ spatial transcriptomics technologies. In addition to being highly scalable, we show that our method, which we call maximization of spatial information (Maxspin), improves accuracy across several spatial transcriptomics platforms and a variety of simulations when compared with a variety of state-of-the-art methods. To further demonstrate the method, we generated in situ spatial transcriptomics data in a renal cell carcinoma sample using the CosMx Spatial Molecular Imager and used Maxspin to reveal novel spatial patterns of tumor cell gene expression.
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Affiliation(s)
| | | | - Youngmi Kim
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Raphael Gottardo
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Biomedical Data Science Center, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
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12
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Talla A, Vasaikar SV, Szeto GL, Lemos MP, Czartoski JL, MacMillan H, Moodie Z, Cohen KW, Fleming LB, Thomson Z, Okada L, Becker LA, Coffey EM, De Rosa SC, Newell EW, Skene PJ, Li X, Bumol TF, Juliana McElrath M, Torgerson TR. Persistent serum protein signatures define an inflammatory subcategory of long COVID. Nat Commun 2023; 14:3417. [PMID: 37296110 PMCID: PMC10252177 DOI: 10.1038/s41467-023-38682-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 04/11/2022] [Accepted: 05/10/2023] [Indexed: 06/12/2023] Open
Abstract
Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or delayed clearance of viral protein or RNA, but the biological differences they represent are not fully understood. Here we evaluate the serum proteome in samples, longitudinally collected from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection, in comparison to samples from symptomatically recovered SARS-CoV-2 infected and uninfected individuals. Our analysis indicates heterogeneity in PASC and identified subsets with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), appear to be the most differentially enriched signaling pathways, distinguishing a group of patients characterized also by a persistent neutrophil activation signature. These findings help to clarify biological diversity within PASC, identify participants with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance, including a protein panel that we propose as having diagnostic utility for differentiating inflammatory and non-inflammatory PASC.
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Affiliation(s)
- Aarthi Talla
- Allen Institute for Immunology, Seattle, WA, USA
| | - Suhas V Vasaikar
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | - Gregory Lee Szeto
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | - Maria P Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hugh MacMillan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Moderna, Cambridge, MA, USA
| | - Lamar B Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lauren Okada
- Allen Institute for Immunology, Seattle, WA, USA
| | | | | | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Xiaojun Li
- Allen Institute for Immunology, Seattle, WA, USA
| | | | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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13
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Oyong DA, Duffy FJ, Neal ML, Du Y, Carnes J, Schwedhelm KV, Hertoghs N, Jun SH, Miller H, Aitchison JD, De Rosa SC, Newell EW, McElrath MJ, McDermott SM, Stuart KD. Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge. PLoS Pathog 2023; 19:e1011051. [PMID: 37195999 PMCID: PMC10228810 DOI: 10.1371/journal.ppat.1011051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/30/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Understanding immune mechanisms that mediate malaria protection is critical for improving vaccine development. Vaccination with radiation-attenuated Plasmodium falciparum sporozoites (PfRAS) induces high level of sterilizing immunity against malaria and serves as a valuable tool for the study of protective mechanisms. To identify vaccine-induced and protection-associated responses during malarial infection, we performed transcriptome profiling of whole blood and in-depth cellular profiling of PBMCs from volunteers who received either PfRAS or noninfectious mosquito bites, followed by controlled human malaria infection (CHMI) challenge. In-depth single-cell profiling of cell subsets that respond to CHMI in mock-vaccinated individuals showed a predominantly inflammatory transcriptome response. Whole blood transcriptome analysis revealed that gene sets associated with type I and II interferon and NK cell responses were increased in prior to CHMI while T and B cell signatures were decreased as early as one day following CHMI in protected vaccinees. In contrast, non-protected vaccinees and mock-vaccinated individuals exhibited shared transcriptome changes after CHMI characterized by decreased innate cell signatures and inflammatory responses. Additionally, immunophenotyping data showed different induction profiles of vδ2+ γδ T cells, CD56+ CD8+ T effector memory (Tem) cells, and non-classical monocytes between protected vaccinees and individuals developing blood-stage parasitemia, following treatment and resolution of infection. Our data provide key insights in understanding immune mechanistic pathways of PfRAS-induced protection and infective CHMI. We demonstrate that vaccine-induced immune response is heterogenous between protected and non-protected vaccinees and that inducted-malaria protection by PfRAS is associated with early and rapid changes in interferon, NK cell and adaptive immune responses. Trial Registration: ClinicalTrials.gov NCT01994525.
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Affiliation(s)
- Damian A. Oyong
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Fergal J. Duffy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ying Du
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Katharine V. Schwedhelm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Nina Hertoghs
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Seong-Hwan Jun
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Helen Miller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - John D. Aitchison
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Evan W. Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Suzanne M. McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kenneth D. Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children’s Research Institute, Seattle, Washington, United States of America
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14
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Wanjalla CN, Gabriel CL, Fuseini H, Bailin SS, Mashayekhi M, Simmons J, Warren CM, Glass DR, Oakes J, Gangula R, Wilfong E, Priest S, Temu T, Newell EW, Pakala S, Kalams SA, Gianella S, Smith D, Harrison DG, Mallal SA, Koethe JR. CD4 + T cells expressing CX3CR1, GPR56, with variable CD57 are associated with cardiometabolic diseases in persons with HIV. Front Immunol 2023; 14:1099356. [PMID: 36865544 PMCID: PMC9971959 DOI: 10.3389/fimmu.2023.1099356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
Persons with HIV (PWH) on long-term antiretroviral therapy (ART) have a higher incidence and prevalence of cardiometabolic diseases attributed, in part, to persistent inflammation despite viral suppression. In addition to traditional risk factors, immune responses to co-infections such as cytomegalovirus (CMV) may play an unappreciated role in cardiometabolic comorbidities and offer new potential therapeutic targets in a subgroup of individuals. We assessed the relationship of CX3CR1+, GPR56+, and CD57+/- T cells (termed CGC+) with comorbid conditions in a cohort of 134 PWH co-infected with CMV on long-term ART. We found that PWH with cardiometabolic diseases (non-alcoholic fatty liver disease, calcified coronary arteries, or diabetes) had higher circulating CGC+CD4+ T cells compared to metabolically healthy PWH. The traditional risk factor most correlated with CGC+CD4+ T cell frequency was fasting blood glucose, as well as starch/sucrose metabolites. While unstimulated CGC+CD4+ T cells, like other memory T cells, depend on oxidative phosphorylation for energy, they exhibited higher expression of carnitine palmitoyl transferase 1A compared to other CD4+ T cell subsets, suggesting a potentially greater capacity for fatty acid β-oxidation. Lastly, we show that CMV-specific T cells against multiple viral epitopes are predominantly CGC+. Together, this study suggests that among PWH, CGC+ CD4+ T cells are frequently CMV-specific and are associated with diabetes, coronary arterial calcium, and non-alcoholic fatty liver disease. Future studies should assess whether anti-CMV therapies could reduce cardiometabolic disease risk in some individuals.
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Affiliation(s)
- Celestine N Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Curtis L Gabriel
- Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Hubaida Fuseini
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Samuel S Bailin
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mona Mashayekhi
- Division of Endocrinology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua Simmons
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christopher M Warren
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - David R Glass
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jared Oakes
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rama Gangula
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Erin Wilfong
- Division of Rheumatology, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stephen Priest
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tecla Temu
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Evan W Newell
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Suman Pakala
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Spyros A Kalams
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Sara Gianella
- Department of Medicine, University of California, San Diego, CA, United States
| | - David Smith
- Department of Medicine, University of California, San Diego, CA, United States
| | - David G Harrison
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Simon A Mallal
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John R Koethe
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Infectious Disease Section, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
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15
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Vitanza NA, Wilson AL, Huang W, Seidel K, Brown C, Gustafson JA, Yokoyama JK, Johnson AJ, Baxter BA, Koning RW, Reid AN, Meechan M, Biery MC, Myers C, Rawlings-Rhea SD, Albert CM, Browd SR, Hauptman JS, Lee A, Ojemann JG, Berens ME, Dun MD, Foster JB, Crotty EE, Leary SE, Cole BL, Perez FA, Wright JN, Orentas RJ, Chour T, Newell EW, Whiteaker JR, Zhao L, Paulovich AG, Pinto N, Gust J, Gardner RA, Jensen MC, Park JR. Intraventricular B7-H3 CAR T Cells for Diffuse Intrinsic Pontine Glioma: Preliminary First-in-Human Bioactivity and Safety. Cancer Discov 2023; 13:114-131. [PMID: 36259971 PMCID: PMC9827115 DOI: 10.1158/2159-8290.cd-22-0750] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 01/16/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) tumors, we designed B7-H3-specific chimeric antigen receptor (CAR) T cells, confirmed their preclinical efficacy, and opened BrainChild-03 (NCT04185038), a first-in-human phase I trial administering repeated locoregional B7-H3 CAR T cells to children with recurrent/refractory CNS tumors and DIPG. Here, we report the results of the first three evaluable patients with DIPG (including two who enrolled after progression), who received 40 infusions with no dose-limiting toxicities. One patient had sustained clinical and radiographic improvement through 12 months on study. Patients exhibited correlative evidence of local immune activation and persistent cerebrospinal fluid (CSF) B7-H3 CAR T cells. Targeted mass spectrometry of CSF biospecimens revealed modulation of B7-H3 and critical immune analytes (CD14, CD163, CSF-1, CXCL13, and VCAM-1). Our data suggest the feasibility of repeated intracranial B7-H3 CAR T-cell dosing and that intracranial delivery may induce local immune activation. SIGNIFICANCE This is the first report of repeatedly dosed intracranial B7-H3 CAR T cells for patients with DIPG and includes preliminary tolerability, the detection of CAR T cells in the CSF, CSF cytokine elevations supporting locoregional immune activation, and the feasibility of serial mass spectrometry from both serum and CSF. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Corresponding Author: Nicholas A. Vitanza, Seattle Children's Research Institute, M/S JMB-8, 1900 9th Avenue, Seattle, WA 98101. Phone: 206-884-4084; E-mail:
| | | | - Wenjun Huang
- Seattle Children's Therapeutics, Seattle, Washington
| | - Kristy Seidel
- Seattle Children's Therapeutics, Seattle, Washington
| | - Christopher Brown
- Seattle Children's Therapeutics, Seattle, Washington.,Therapeutic Cell Production Core, Seattle Children's Research Institute, Seattle, Washington
| | | | | | | | | | | | | | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Matthew C. Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Catherine M. Albert
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Samuel R. Browd
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jason S. Hauptman
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Amy Lee
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jeffrey G. Ojemann
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Michael E. Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Matthew D. Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, Callaghan, Australia.,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Jessica B. Foster
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erin E. Crotty
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Sarah E.S. Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Bonnie L. Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Francisco A. Perez
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Jason N. Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Rimas J. Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Tony Chour
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan W. Newell
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Navin Pinto
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Juliane Gust
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, Washington
| | - Rebecca A. Gardner
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
| | | | - Julie R. Park
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
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16
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Fehlings M, Kim L, Guan X, Yuen K, Tafazzol A, Sanjabi S, Zill OA, Rishipathak D, Wallace A, Nardin A, Ma S, Milojkovic A, Newell EW, Mariathasan S, Yadav M. Single-cell analysis reveals clonally expanded tumor-associated CD57 + CD8 T cells are enriched in the periphery of patients with metastatic urothelial cancer responding to PD-L1 blockade. J Immunother Cancer 2022; 10:jitc-2022-004759. [PMID: 35981786 PMCID: PMC9394212 DOI: 10.1136/jitc-2022-004759] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND A growing body of evidence suggests that T-cell responses against neoantigens are critical regulators of response to immune checkpoint blockade. We previously showed that circulating neoantigen-specific CD8 T cells in patients with lung cancer responding to anti-Programmed death-ligand 1 (PD-L1) (atezolizumab) exhibit a unique phenotype with high expression of CD57, CD244, and KLRG1. Here, we extended our analysis on neoantigen-specific CD8 T cells to patients with metastatic urothelial cancer (mUC) and further profiled total CD8 T cells to identify blood-based predictive biomarkers of response to atezolizumab. METHODS We identified tumor neoantigens from 20 patients with mUC and profiled their peripheral CD8 T cells using highly multiplexed combinatorial tetramer staining. Another set of patients with mUC treated with atezolizumab (n=30) or chemotherapy (n=40) were selected to profile peripheral CD8 T cells by mass cytometry. Using single-cell transcriptional analysis (single-cell RNA sequencing (scRNA-seq)), together with CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) and paired T-cell receptor (TCR) sequencing, we further characterized peripheral CD8 T cells in a subset of patients (n=16). RESULTS High frequency of CD57 was observed in neoantigen-specific CD8 T cells in patients with mUC responding to atezolizumab. Extending these findings to bulk CD8 T cells, we found higher frequency of CD57 expressing CD8 T cells before treatment in patients responding to atezolizumab (n=20, p<0.01) but not to chemotherapy. These findings were corroborated in a validation cohort (n=30, p<0.01) and notably were independent of known biomarkers of response. scRNA-seq analysis identified a clonally expanded cluster enriched within CD57+ CD8 T cells in responding patients characterized by higher expression of genes associated with activation, cytotoxicity, and tissue-resident memory markers. Furthermore, compared with CD57- CD8 T cells, TCRs of CD57+ CD8 T cells showed increased overlap with the TCR repertoire of tumor-infiltrating T cells. CONCLUSIONS Collectively, we show high frequencies of CD57 among neoantigen-specific and bulk CD8 T cells in patients responding to atezolizumab. The TCR repertoire overlap between peripheral CD57+ CD8 T cells and tumor-infiltrating lymphocytes suggest that accumulation of peripheral CD57+ CD8 T cells is reflective of an ongoing antitumor T-cell response. Our findings provide evidence and rationale for using circulating CD8 T cells expressing CD57 as a readily accessible blood-based biomarker for selecting patients with mUC for atezolizumab therapy.
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Affiliation(s)
| | - Leesun Kim
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Xiangnan Guan
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Kobe Yuen
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Alireza Tafazzol
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Shomyseh Sanjabi
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Oliver A Zill
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Deepali Rishipathak
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Andrew Wallace
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | | | | | | | - Evan W Newell
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sanjeev Mariathasan
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | - Mahesh Yadav
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, California, USA
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17
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Li S, Zhuang S, Heit A, Koo SL, Tan AC, Chow IT, Kwok WW, Tan IB, Tan DS, Simoni Y, Newell EW. Bystander CD4 + T cells infiltrate human tumors and are phenotypically distinct. Oncoimmunology 2022; 11:2012961. [PMID: 36524209 PMCID: PMC9746624 DOI: 10.1080/2162402x.2021.2012961] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tumor-specific T cells likely underpin effective immune checkpoint-blockade therapies. Yet, most studies focus on Treg cells and CD8+ tumor-infiltrating lymphocytes (TILs). Here, we study CD4+ TILs in human lung and colorectal cancers and observe that non-Treg CD4+ TILs average more than 70% of total CD4+ TILs in both cancer types. Leveraging high dimensional analyses including mass cytometry, we reveal that CD4+ TILs are phenotypically heterogeneous, within each tumor and across patients. Consistently, we find different subsets of CD4+ TILs showing characteristics of effectors, tissue resident memory (Trm) or exhausted cells (expressing PD-1, CTLA-4 and CD39). In both cancer types, the frequencies of CD39- non-Treg CD4+ TILs strongly correlate with frequencies of CD39- CD8+ TILs, which we and others have previously shown to be enriched for cells specific for cancer-unrelated antigens (bystanders). Ex-vivo, we demonstrate that CD39- CD4+ TILs can be specific for cancer-unrelated antigens, such as HCMV epitopes. Overall, our findings highlight that CD4+ TILs can also recognize cancer-unrelated antigens and suggest measuring CD39 expression as a straightforward way to quantify or isolate bystander CD4+ T cells.
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Affiliation(s)
- Shamin Li
- Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Summer Zhuang
- Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Antja Heit
- Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Si-Lin Koo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore,Division of Medical Oncology, National Cancer Centre Singapore (NCCS), Singapore, Singapore
| | - Aaron C. Tan
- Division of Medical Oncology, National Cancer Centre Singapore (NCCS), Singapore, Singapore
| | - I-Ting Chow
- Agency for Science Technology and Research (A*Star), Genome Institute of Singapore (GIS), Singapore, Singapore
| | - William W. Kwok
- Agency for Science Technology and Research (A*Star), Genome Institute of Singapore (GIS), Singapore, Singapore
| | - Iain Beehuat Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore,Division of Medical Oncology, National Cancer Centre Singapore (NCCS), Singapore, Singapore
| | | | - Yannick Simoni
- Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA,Université de Paris, Institut Cochin INSERM U1016, Paris, France,CONTACT Yannick Simoni Université de Paris, Institut Cochin INSERM U1016, 22 Rue Mechain, Paris75014, France
| | - Evan W. Newell
- Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA,Evan W. Newell Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, 1100 Fairview Ave. N., Mail Stop S2-204, Seattle, WA98109, USA
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18
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Yeh AC, Varelias A, Reddy A, Barone SM, Olver SD, Chilson K, Onstad LE, Ensbey KS, Henden AS, Samson L, Jaeger CA, Bi T, Dahlman KB, Kim TK, Zhang P, Degli-Esposti MA, Newell EW, Jagasia MH, Irish JM, Lee SJ, Hill GR. CMV exposure drives long-term CD57+ CD4 memory T-cell inflation following allogeneic stem cell transplant. Blood 2021; 138:2874-2885. [PMID: 34115118 PMCID: PMC8718626 DOI: 10.1182/blood.2020009492] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/22/2021] [Indexed: 01/01/2023] Open
Abstract
Donor and recipient cytomegalovirus (CMV) serostatus correlate with transplant-related mortality that is associated with reduced survival following allogeneic stem cell transplant (SCT). Prior epidemiologic studies have suggested that CMV seronegative recipients (R-) receiving a CMV-seropositive graft (D+) experience inferior outcomes compared with other serostatus combinations, an observation that appears independent of viral reactivation. We therefore investigated the hypothesis that prior donor CMV exposure irreversibly modifies immunologic function after SCT. We identified a CD4+/CD57+/CD27- T-cell subset that was differentially expressed between D+ and D- transplants and validated results with 120 patient samples. This T-cell subset represents an average of 2.9% (D-/R-), 18% (D-/R+), 12% (D+/R-), and 19.6% (D+/R+) (P < .0001) of the total CD4+ T-cell compartment and stably persists for at least several years post-SCT. Even in the absence of CMV reactivation post-SCT, D+/R- transplants displayed a significant enrichment of these cells compared with D-/R- transplants (P = .0078). These are effector memory cells (CCR7-/CD45RA+/-) that express T-bet, Eomesodermin, granzyme B, secrete Th1 cytokines, and are enriched in CMV-specific T cells. These cells are associated with decreased T-cell receptor diversity (P < .0001) and reduced proportions of major histocompatibility class (MHC) II expressing classical monocytes (P < .0001), myeloid (P = .024), and plasmacytoid dendritic cells (P = .0014). These data describe a highly expanded CD4+ T-cell population and putative mechanisms by which prior donor or recipient CMV exposure may create a lasting immunologic imprint following SCT, providing a rationale for using D- grafts for R- transplant recipients.
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Affiliation(s)
- Albert C Yeh
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA
| | - Antiopi Varelias
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Facuty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Stuart D Olver
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kate Chilson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Lynn E Onstad
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kathleen S Ensbey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Andrea S Henden
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Luke Samson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Carla A Jaeger
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Timothy Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kimberly B Dahlman
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; and
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; and
| | - Ping Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Madan H Jagasia
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; and
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA
| | - Geoffrey R Hill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA
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19
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Abstract
T cells mediate anti-tumor immune responses and are the key target of immune checkpoint therapy, but they can also promote immune tolerance. A clear understanding of the specific contributions and biology of different T cell subsets is required to fully harness the curative potential of immunotherapies. Experts discuss the state of the field and key challenges for moving forward.
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20
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Reales-Calderon JA, Tso GHW, Tan ASM, Hor PX, Böhme J, Teng KWW, Newell EW, Singhal A, Pavelka N. Gut-Evolved Candida albicans Induces Metabolic Changes in Neutrophils. Front Cell Infect Microbiol 2021; 11:743735. [PMID: 34881192 PMCID: PMC8645939 DOI: 10.3389/fcimb.2021.743735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 12/02/2022] Open
Abstract
Serial passaging of the human fungal pathogen Candida albicans in the gastrointestinal tract of antibiotics-treated mice selects for virulence-attenuated strains. These gut-evolved strains protect the host from infection by a wide range of pathogens via trained immunity. Here, we further investigated the molecular and cellular mechanisms underlying this innate immune memory. Both Dectin-1 (the main receptor for β-glucan; a well-described immune training molecule in the fungal cell wall) and Nod2 (a receptor described to mediate BCG-induced trained immunity), were redundant for the protection induced by gut-evolved C. albicans against a virulent C. albicans strain, suggesting that gut-evolved C. albicans strains induce trained immunity via other pathways. Cytometry by time of flight (CyTOF) analysis of mouse splenocytes revealed that immunization with gut-evolved C. albicans resulted in an expansion of neutrophils and a reduction in natural killer (NK) cells, but no significant numeric changes in monocytes, macrophages or dendritic cell populations. Systemic depletion of phagocytes or neutrophils, but not of macrophages or NK cells, reduced protection mediated by gut-evolved C. albicans. Splenocytes and bone marrow cells of mice immunized with gut-evolved C. albicans demonstrated metabolic changes. In particular, splenic neutrophils displayed significantly elevated glycolytic and respiratory activity in comparison to those from mock-immunized mice. Although further investigation is required for fully deciphering the trained immunity mechanism induced by gut-evolved C. albicans strains, this data is consistent with the existence of several mechanisms of trained immunity, triggered by different training stimuli and involving different immune molecules and cell types.
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Affiliation(s)
| | - Gloria H W Tso
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Alrina S M Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Pei Xiang Hor
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Julia Böhme
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Karen W W Teng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Amit Singhal
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,ASTAR Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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21
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Becht E, Tolstrup D, Dutertre CA, Morawski PA, Campbell DJ, Ginhoux F, Newell EW, Gottardo R, Headley MB. High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning. Sci Adv 2021; 7:eabg0505. [PMID: 34550730 PMCID: PMC8457665 DOI: 10.1126/sciadv.abg0505] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/14/2021] [Indexed: 06/03/2023]
Abstract
Modern immunologic research increasingly requires high-dimensional analyses to understand the complex milieu of cell types that comprise the tissue microenvironments of disease. To achieve this, we developed Infinity Flow combining hundreds of overlapping flow cytometry panels using machine learning to enable the simultaneous analysis of the coexpression patterns of hundreds of surface-expressed proteins across millions of individual cells. In this study, we demonstrate that this approach allows the comprehensive analysis of the cellular constituency of the steady-state murine lung and the identification of previously unknown cellular heterogeneity in the lungs of melanoma metastasis–bearing mice. We show that by using supervised machine learning, Infinity Flow enhances the accuracy and depth of clustering or dimensionality reduction algorithms. Infinity Flow is a highly scalable, low-cost, and accessible solution to single-cell proteomics in complex tissues.
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Affiliation(s)
- Etienne Becht
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Tolstrup
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles-Antoine Dutertre
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
| | - Peter A. Morawski
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Daniel J. Campbell
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Evan W. Newell
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark B. Headley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
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22
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Blériot C, Barreby E, Dunsmore G, Ballaire R, Chakarov S, Ficht X, De Simone G, Andreata F, Fumagalli V, Guo W, Wan G, Gessain G, Khalilnezhad A, Zhang XM, Ang N, Chen P, Morgantini C, Azzimato V, Kong WT, Liu Z, Pai R, Lum J, Shihui F, Low I, Xu C, Malleret B, Kairi MFM, Balachander A, Cexus O, Larbi A, Lee B, Newell EW, Ng LG, Phoo WW, Sobota RM, Sharma A, Howland SW, Chen J, Bajenoff M, Yvan-Charvet L, Venteclef N, Iannacone M, Aouadi M, Ginhoux F. A subset of Kupffer cells regulates metabolism through the expression of CD36. Immunity 2021; 54:2101-2116.e6. [PMID: 34469775 DOI: 10.1016/j.immuni.2021.08.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/27/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Tissue macrophages are immune cells whose phenotypes and functions are dictated by origin and niches. However, tissues are complex environments, and macrophage heterogeneity within the same organ has been overlooked so far. Here, we used high-dimensional approaches to characterize macrophage populations in the murine liver. We identified two distinct populations among embryonically derived Kupffer cells (KCs) sharing a core signature while differentially expressing numerous genes and proteins: a major CD206loESAM- population (KC1) and a minor CD206hiESAM+ population (KC2). KC2 expressed genes involved in metabolic processes, including fatty acid metabolism both in steady-state and in diet-induced obesity and hepatic steatosis. Functional characterization by depletion of KC2 or targeted silencing of the fatty acid transporter Cd36 highlighted a crucial contribution of KC2 in the liver oxidative stress associated with obesity. In summary, our study reveals that KCs are more heterogeneous than anticipated, notably describing a subpopulation wired with metabolic functions.
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Affiliation(s)
- Camille Blériot
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Inserm U1015, Gustave Roussy, Villejuif 94800, France.
| | - Emelie Barreby
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | | | | | - Svetoslav Chakarov
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xenia Ficht
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giorgia De Simone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Valeria Fumagalli
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Wei Guo
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guochen Wan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Gregoire Gessain
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Ahad Khalilnezhad
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Program, Yong Loo Lin School of Medicine, Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore
| | - Xiao Meng Zhang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Nicholas Ang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Ping Chen
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | - Cecilia Morgantini
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | - Valerio Azzimato
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | - Wan Ting Kong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rhea Pai
- Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Foo Shihui
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Ivy Low
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Connie Xu
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Program, Yong Loo Lin School of Medicine, Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore
| | - Muhammad Faris Mohd Kairi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Akhila Balachander
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Olivier Cexus
- Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Program, Yong Loo Lin School of Medicine, Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore
| | - Wint Wint Phoo
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Ankur Sharma
- Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Shanshan W Howland
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Marc Bajenoff
- Aix Marseille University, CNRS, INSERM, CIML, Marseille 13288, France
| | | | - Nicolas Venteclef
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, IMMEDIAB Laboratory, Paris 75006, France
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy; Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Myriam Aouadi
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Huddinge 14157, Sweden
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Microbiology and Immunology, Immunology Translational Research Program, Yong Loo Lin School of Medicine, Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore.
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23
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Ma T, Ryu H, McGregor M, Babcock B, Neidleman J, Xie G, George AF, Frouard J, Murray V, Gill G, Ghosn E, Newell EW, Lee SA, Roan NR. Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8 + T Cells during Convalescence. J Immunol 2021; 207:1344-1356. [PMID: 34389625 PMCID: PMC8763019 DOI: 10.4049/jimmunol.2100465] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/28/2021] [Indexed: 12/31/2022]
Abstract
CD8+ T cells can potentiate long-lived immunity against COVID-19. We screened longitudinally-sampled convalescent human donors against SARS-CoV-2 tetramers and identified a participant with an immunodominant response against residues 322 to 311 of nucleocapsid (Nuc322-331), a peptide conserved in all variants of concern reported to date. We conducted 38-parameter cytometry by time of flight on tetramer-identified Nuc322-331-specific CD8+ T cells and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins, and took 32 serological measurements. We discovered a coordination of the Nuc322-331-specific CD8+ T response with both the CD4+ T cell and Ab pillars of adaptive immunity. Over the approximately six month period of convalescence monitored, we observed a slow and progressive decrease in the activation state and polyfunctionality of Nuc322-331-specific CD8+ T cells, accompanied by an increase in their lymph node-homing and homeostatic proliferation potential. These results suggest that following a typical case of mild COVID-19, SARS-CoV-2-specific CD8+ T cells not only persist but continuously differentiate in a coordinated fashion well into convalescence into a state characteristic of long-lived, self-renewing memory.
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Affiliation(s)
- Tongcui Ma
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Matthew McGregor
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Benjamin Babcock
- Department of Medicine, Lowance Center for Human Immunology, Emory Vaccine Center, Emory University, Atlanta, GA
| | - Jason Neidleman
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Guorui Xie
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Ashley F George
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Julie Frouard
- Gladstone Institutes, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Victoria Murray
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, CA; and
| | - Gurjot Gill
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, CA; and
| | - Eliver Ghosn
- Department of Medicine, Lowance Center for Human Immunology, Emory Vaccine Center, Emory University, Atlanta, GA
- Department of Pediatrics, Lowance Center for Human Immunology, Emory Vaccine Center, Emory University, Atlanta, GA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, CA; and
| | - Nadia R Roan
- Gladstone Institutes, San Francisco, CA;
- Department of Urology, University of California San Francisco, San Francisco, CA
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24
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Talla A, Vasaikar SV, Lemos MP, Moodie Z, Lee Pebworth MP, Henderson KE, Cohen KW, Czartoski JL, Lai L, Suthar MS, Heubeck AT, Genge PC, Roll CR, Weiss M, Reading J, Kondza N, MacMillan H, Fong OC, Thomson ZJ, Graybuck LT, Okada LY, Newell EW, Coffey EM, Meijer P, Becker LA, De Rosa SC, Skene PJ, Torgerson TR, Li XJ, Szeto GL, McElrath MJ, Bumol TF. Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence. bioRxiv 2021:2021.05.26.442666. [PMID: 34075380 PMCID: PMC8168393 DOI: 10.1101/2021.05.26.442666] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
SARS-CoV-2 has infected over 200 million and caused more than 4 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID-19 beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive immune activation that differed in character by age (young vs. old). We then characterized signals associated with recovery and convalescence to define and validate a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).
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25
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Rouers A, Chng MHY, Lee B, Rajapakse MP, Kaur K, Toh YX, Sathiakumar D, Loy T, Thein TL, Lim VW, Singhal A, Yeo TW, Leo YS, Vora KA, Casimiro D, Lim B, Tucker-Kellogg L, Rivino L, Newell EW, Fink K. Immune cell phenotypes associated with disease severity and long-term neutralizing antibody titers after natural dengue virus infection. Cell Rep Med 2021; 2:100278. [PMID: 34095880 PMCID: PMC8149372 DOI: 10.1016/j.xcrm.2021.100278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/08/2021] [Accepted: 04/21/2021] [Indexed: 12/20/2022]
Abstract
Prior immunological exposure to dengue virus can be both protective and disease-enhancing during subsequent infections with different dengue virus serotypes. We provide here a systematic, longitudinal analysis of B cell, T cell, and antibody responses in the same patients. Antibody responses as well as T and B cell activation differentiate primary from secondary responses. Hospitalization is associated with lower frequencies of activated, terminally differentiated T cells and higher percentages of effector memory CD4 T cells. Patients with more severe disease tend to have higher percentages of plasmablasts. This does not translate into long-term antibody titers, since neutralizing titers after 6 months correlate with percentages of specific memory B cells, but not with acute plasmablast activation. Overall, our unbiased analysis reveals associations between cellular profiles and disease severity, opening opportunities to study immunopathology in dengue disease and the potential predictive value of these parameters.
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Affiliation(s)
- Angeline Rouers
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
| | - Melissa Hui Yen Chng
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Menaka P. Rajapakse
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Kaval Kaur
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Ying Xiu Toh
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Durgalakshmi Sathiakumar
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Thomas Loy
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tun-Linn Thein
- National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Vanessa W.X. Lim
- National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Amit Singhal
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
| | - Tsin Wen Yeo
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
- Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore 308442, Singapore
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
- Tan Tock Seng Hospital, Singapore 308433, Singapore
- Yong Loo Lin School of Medicine, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, Singapore 117549, Singapore
| | - Kalpit A. Vora
- Department of Infectious Diseases and Vaccines Research, Merck, Kenilworth, NJ, USA
| | - Danilo Casimiro
- Department of Infectious Diseases and Vaccines Research, Merck, Kenilworth, NJ, USA
| | - Bing Lim
- Merck Sharp & Dohme Translational Medicine Research Centre, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Lisa Tucker-Kellogg
- Cancer and Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Laura Rivino
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Evan W. Newell
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- Corresponding author
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26
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Yeong J, Suteja L, Simoni Y, Lau KW, Tan AC, Li HH, Lim S, Loh JH, Wee FYT, Nerurkar SN, Takano A, Tan EH, Lim TKH, Newell EW, Tan DSW. Intratumoral CD39 +CD8 + T Cells Predict Response to Programmed Cell Death Protein-1 or Programmed Death Ligand-1 Blockade in Patients With NSCLC. J Thorac Oncol 2021; 16:1349-1358. [PMID: 33975004 DOI: 10.1016/j.jtho.2021.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Programmed cell death protein-1 (PD-1) and programmed death-ligand 1 (PD-L1) blockade is currently widely used in the treatment of metastatic NSCLC. Despite available biomarker stratification, clinical responses vary. Thus, the search for novel biomarkers with improved response prediction is ongoing. Previously, using mass cytometry or cytometry by time-of-flight (CyTOF), our group demonstrated that CD39+CD8+ immune cells represent tumor antigen-specific, cytotoxic T cells in treatment-naive NSCLC. We hypothesized that accurate quantitation of this T cell subset would predict immunotherapy outcome. METHODS To translate this to a clinical setting, the present study compared CyTOF data with a range of clinically relevant methods, including conventional immunohistochemistry (IHC), multiplex IHC or immunofluorescence (mIHC), and gene expression assay by NanoString. RESULTS Quantification using mIHC but not conventional IHC or NanoString correlated with the CyTOF results. The specificity and sensitivity of mIHC were then evaluated in a separate retrospective NSCLC cohort. CD39+CD8+ T cell proportion, as determined by mIHC, successfully stratified responders and nonresponders to PD-1 or PD-L1 inhibitors (objective response rate of 63.6%, compared with 0% for the negative group). This predictive capability was independent from other confounding factors, such as total CD8+ T cell proportion, CD39+ lymphocyte proportion, PD-L1 positivity, EGFR mutation status, and other clinicopathologic parameters. CONCLUSIONS Our results suggest that the mIHC platform is a clinically relevant method to evaluate CD39+CD8+ T cell proportion and that this marker can serve as a potential biomarker that predicts response to PD-1 or PD-L1 blockade in patients with NSCLC. Further validation in additional NSCLC cohorts is warranted.
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Affiliation(s)
- Joe Yeong
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Division of Pathology, Singapore General Hospital, Singapore
| | - Lisda Suteja
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Yannick Simoni
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kah Weng Lau
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore; Division of Pathology, Singapore General Hospital, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Hui Hua Li
- Division of Medicine, Singapore General Hospital, Singapore; Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore
| | - Sherlly Lim
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Jie Hua Loh
- Division of Pathology, Singapore General Hospital, Singapore
| | - Felicia Y T Wee
- Division of Pathology, Singapore General Hospital, Singapore
| | | | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Tony K H Lim
- Division of Pathology, Singapore General Hospital, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.
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27
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Chuntova P, Chow F, Watchmaker PB, Galvez M, Heimberger AB, Newell EW, Diaz A, DePinho RA, Li MO, Wherry EJ, Mitchell D, Terabe M, Wainwright DA, Berzofsky JA, Herold-Mende C, Heath JR, Lim M, Margolin KA, Chiocca EA, Kasahara N, Ellingson BM, Brown CE, Chen Y, Fecci PE, Reardon DA, Dunn GP, Liau LM, Costello JF, Wick W, Cloughesy T, Timmer WC, Wen PY, Prins RM, Platten M, Okada H. Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank. Neuro Oncol 2021; 23:356-375. [PMID: 33367885 PMCID: PMC7992879 DOI: 10.1093/neuonc/noaa277] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer immunotherapy has made remarkable advances with over 50 separate Food and Drug Administration (FDA) approvals as first- or second-line indications since 2015. These include immune checkpoint blocking antibodies, chimeric antigen receptor-transduced T cells, and bispecific T-cell-engaging antibodies. While multiple cancer types now benefit from these immunotherapies, notable exceptions thus far include brain tumors, such as glioblastoma. As such, it seems critical to gain a better understanding of unique mechanistic challenges underlying the resistance of malignant gliomas to immunotherapy, as well as to acquire insights into the development of future strategies. An Immuno-Oncology Think Tank Meeting was held during the 2019 Annual Society for Neuro-Oncology Scientific Conference. Discussants in the fields of neuro-oncology, neurosurgery, neuro-imaging, medical oncology, and cancer immunology participated in the meeting. Sessions focused on topics such as the tumor microenvironment, myeloid cells, T-cell dysfunction, cellular engineering, and translational aspects that are critical and unique challenges inherent with primary brain tumors. In this review, we summarize the discussions and the key messages from the meeting, which may potentially serve as a basis for advancing the field of immune neuro-oncology in a collaborative manner.
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Affiliation(s)
- Pavlina Chuntova
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Frances Chow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Mildred Galvez
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California
| | - Amy B Heimberger
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Aaron Diaz
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - E John Wherry
- Department of Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Duane Mitchell
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, Florida
| | - Masaki Terabe
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Derek A Wainwright
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jay A Berzofsky
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | | | - Michael Lim
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kim A Margolin
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Benjamin M Ellingson
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Christine E Brown
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, California
| | - Yvonne Chen
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, California
| | - Peter E Fecci
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - David A Reardon
- Department of Medicine/Medical Oncology, Harvard Medical School, Boston, Massachusetts
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Wolfgang Wick
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - William C Timmer
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Robert M Prins
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, MCTN, University of Heidelberg, Mannheim, Germany.,DKTK CCU Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hideho Okada
- Department of Neurological Surgery, UCSF, San Francisco, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
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28
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Kared H, Redd AD, Bloch EM, Bonny TS, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell EW, Bettinotti MP, Benner SE, Patel EU, Littlefield K, Laeyendecker O, Shoham S, Sullivan D, Casadevall A, Pekosz A, Nardin A, Fehlings M, Tobian AA, Quinn TC. SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals. J Clin Invest 2021; 131:145476. [PMID: 33427749 DOI: 10.1172/jci145476] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Characterization of the T cell response in individuals who recover from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 coronavirus disease 2019 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis and from humoral and inflammatory responses. There were 132 SARS-CoV-2-specific CD8+ T cell responses detected across 6 different HLAs, corresponding to 52 unique epitope reactivities. CD8+ T cell responses were detected in almost all convalescent individuals and were directed against several structural and nonstructural target epitopes from the entire SARS-CoV-2 proteome. A unique phenotype for SARS-CoV-2-specific T cells was observed that was distinct from other common virus-specific T cells detected in the same cross-sectional sample and characterized by early differentiation kinetics. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem cell and transitional memory states (subsets), which may be key to developing durable protection.
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Affiliation(s)
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tania S Bonny
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - Evan W Newell
- ImmunoScape, Singapore, Singapore.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Maria P Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eshan U Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Epidemiology and
| | - Kirsten Littlefield
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | | | - David Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Aaron Ar Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
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29
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Galletti G, De Simone G, Mazza EMC, Puccio S, Mezzanotte C, Bi TM, Davydov AN, Metsger M, Scamardella E, Alvisi G, De Paoli F, Zanon V, Scarpa A, Camisa B, Colombo FS, Anselmo A, Peano C, Polletti S, Mavilio D, Gattinoni L, Boi SK, Youngblood BA, Jones RE, Baird DM, Gostick E, Llewellyn-Lacey S, Ladell K, Price DA, Chudakov DM, Newell EW, Casucci M, Lugli E. Two subsets of stem-like CD8 + memory T cell progenitors with distinct fate commitments in humans. Nat Immunol 2020; 21:1552-1562. [PMID: 33046887 PMCID: PMC7610790 DOI: 10.1038/s41590-020-0791-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8+ memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8+ memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8+ memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.
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Affiliation(s)
- Giovanni Galletti
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Gabriele De Simone
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Emilia M C Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Simone Puccio
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Claudia Mezzanotte
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Maria Metsger
- Central European Institute of Technology, Brno, Czech Republic
| | - Eloise Scamardella
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Giorgia Alvisi
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Federica De Paoli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Veronica Zanon
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Alice Scarpa
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Barbara Camisa
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico S Colombo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Achille Anselmo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Milan, Italy
- Genomic Unit, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Sara Polletti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Luca Gattinoni
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Regensburg Center for Interventional Immunology, Regensburg, Germany
- University of Regensburg, Regensburg, Germany
| | - Shannon K Boi
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Rhiannon E Jones
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Monica Casucci
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.
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30
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Kared H, Redd AD, Bloch EM, Bonny TS, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell EW, Bettinotti MP, Benner SE, Patel EU, Littlefield K, Laeyendecker O, Shoham S, Sullivan D, Casadevall A, Pekosz A, Nardin A, Fehlings M, Tobian AAR, Quinn TC. CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation. bioRxiv 2020:2020.10.08.330688. [PMID: 33052343 PMCID: PMC7553170 DOI: 10.1101/2020.10.08.330688] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterization of the T cell response in individuals who recover from SARS-CoV-2 infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 COVID-19 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis, humoral and inflammatory responses. 132 distinct SARS-CoV-2-specific CD8+ T cell epitope responses across six different HLAs were detected, corresponding to 52 unique reactivities. T cell responses were directed against several structural and non-structural virus proteins. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem-cell and transitional memory states, subsets, which may be key to developing durable protection.
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Affiliation(s)
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tania S. Bonny
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Evan W Newell
- ImmunoScape Pte Ltd, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maria P. Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E. Benner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eshan U. Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kirsten Littlefield
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Aaron AR Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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31
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DeGottardi Q, Gates TJ, Yang J, James EA, Malhotra U, Chow IT, Simoni Y, Fehlings M, Newell EW, DeBerg HA, Kwok WW. Ontogeny of different subsets of yellow fever virus-specific circulatory CXCR5 + CD4 + T cells after yellow fever vaccination. Sci Rep 2020; 10:15686. [PMID: 32973217 PMCID: PMC7519049 DOI: 10.1038/s41598-020-72610-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
Monitoring the frequency of circulatory CXCR5+ (cCXCR5+) CD4+ T cells in periphery blood provides a potential biomarker to draw inferences about T follicular helper (TFH) activity within germinal center. However, cCXCR5+ T cells are highly heterogeneous in their expression of ICOS, PD1 and CD38 and the relationship between different cCXCR5 subsets as delineated by these markers remains unclear. We applied class II tetramer reagents and mass cytometry to investigate the ontogeny of different subsets of cCXCR5+ T cell following yellow fever immunization. Through unsupervised analyses of mass cytometry data, we show yellow fever virus-specific cCXCR5 T cells elicited by vaccination were initially CD38+ICOS+PD1+, but then transitioned to become CD38+ICOS-PD1+ and CD38-ICOS-PD1+ before coming to rest as a CD38-ICOS-PD1- subset. These results imply that most antigen-specific cCXCR5+ T cells, including the CD38-ICOS-PD1- CXCR5+ T cells are derived from the CXCR5+CD38+ICOS+PD1+ subset, the subset that most resembles preTFH/TFH in the germinal center.
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Affiliation(s)
- Quinn DeGottardi
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA.,Adaptive Biotechnologies, Seattle, WA, USA
| | - Theresa J Gates
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA
| | - Junbao Yang
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA.,Cs-Bay Therapeutics, Newark, CA, USA
| | - Eddie A James
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA
| | - Uma Malhotra
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA.,Virginia Mason Hospital, Seattle, WA, USA
| | - I-Ting Chow
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA
| | - Yannick Simoni
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Fehlings
- Singapore Immunology Network, Agency for Science Research and Technology, Singapore, Singapore
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hannah A DeBerg
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA
| | - William W Kwok
- Benaroya Research Institute At Virginia Mason Medical Center, 1201, 9th Ave, Seattle, WA, 98101, USA. .,Department of Medicine, University of Washington, Seattle, WA, USA.
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32
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Simoni Y, Becht E, Li S, Loh CY, Yeong JPS, Lim TKH, Takano A, Tan DSW, Newell EW. Partial absence of PD-1 expression by tumor-infiltrating EBV-specific CD8 + T cells in EBV-driven lymphoepithelioma-like carcinoma. Clin Transl Immunology 2020; 9:e1175. [PMID: 32995000 PMCID: PMC7503213 DOI: 10.1002/cti2.1175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/15/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Objectives Lymphoepithelioma‐like carcinoma (LELC) is an uncommon lung cancer, typically observed in young, non‐smoking Asian populations. LELC is associated with Epstein–Barr virus (EBV) infection of lung tumor cells of epithelial origin, suggesting a carcinogenic role of EBV as observed in nasopharyngeal carcinoma (NPC). Here, we studied the antigen specificity and phenotype of EBV‐specific CD8+ T cells in blood and tumor of one LELC patient positive for EBV infection in lung tumor cells. Methods Using multiplex MHC class I tetramers, mass cytometry and mRNA sequencing, we studied EBV‐specific CD8+ T cells at the transcriptomic and phenotypic levels in blood and tumor tissues of the LELC patient. Results Lymphoepithelioma‐like carcinoma lung tumor cells were positive for EBV infection. In both blood and tumor tissues, we detected two populations of EBV‐specific CD8+ T cells targeting the EBV lytic cycle proteins: BRLF1 and BMLF1. Transcriptomic analyses of these two populations in the tumor, which can be considered as tumor‐specific, revealed their distinct exhausted profile and polyclonal TCR repertoire. High‐dimensional phenotypical analysis revealed the distinct phenotype of these cells between blood and tumor tissues. In tumor tissue, EBV‐specific CD8+ TILs were phenotypically heterogeneous, but consistently expressed CD39. Unexpectedly, although the LELC tumor cells expressed abundant PD‐L1, these tumor‐specific CD8+ tumor‐infiltrating lymphocytes (TILs) mostly did not express PD‐1. Conclusion Epstein–Barr virus‐specific CD8+ TILs in EBV‐driven tumor are heterogeneous and partially lack PD‐1 expression, suggesting that anti‐PD1/PD‐L1 immunotherapy may not be an appropriate strategy for disinhibiting EBV‐specific cells in the treatment of LELC patients.
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Affiliation(s)
- Yannick Simoni
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,ImmunoScape Pte Ltd Singapore
| | - Etienne Becht
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Shamin Li
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Chiew Yee Loh
- Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Joe Poh Sheng Yeong
- Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Angela Takano
- Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology National Cancer Centre Singapore (NCCS) Singapore.,Agency for Science, Technology and Research (ASTAR) Genome Institute of Singapore (GIS) Singapore
| | - Evan W Newell
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,Senior Corresponding Author
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33
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Ng HHM, Lee RY, Goh S, Tay ISY, Lim X, Lee B, Chew V, Li H, Tan B, Lim S, Lim JCT, Au B, Loh JJH, Saraf S, Connolly JE, Loh T, Leow WQ, Lee JJX, Toh HC, Malavasi F, Lee SY, Chow P, Newell EW, Choo SP, Tai D, Yeong J, Lim TKH. Immunohistochemical scoring of CD38 in the tumor microenvironment predicts responsiveness to anti-PD-1/PD-L1 immunotherapy in hepatocellular carcinoma. J Immunother Cancer 2020; 8:jitc-2020-000987. [PMID: 32847986 PMCID: PMC7451957 DOI: 10.1136/jitc-2020-000987] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-associated mortality globally. Immune-checkpoint blockade (ICB) is one of the systemic therapy options for HCC. However, response rates remain low, necessitating robust predictive biomarkers. In the present study, we examined the expression of CD38, a molecule involved in the immunosuppressive adenosinergic pathway, on immune cells present in the tumor microenvironment. We then investigated the association between CD38 and ICB treatment outcomes in advanced HCC. Methods Clinically annotated samples from 49 patients with advanced HCC treated with ICB were analyzed for CD38 expression using immunohistochemistry (IHC), multiplex immunohistochemistry/immunofluorescence (mIHC/IF) and multiplex cytokine analysis. Results IHC and mIHC/IF analyses revealed that higher intratumoral CD38+ cell proportion was strongly associated with improved response to ICB. The overall response rates to ICB was significantly higher among patients with high proportion of total CD38+cells compared with patients with low proportion (43.5% vs 3.9%, p=0.019). Higher responses seen among patients with a high intratumoral CD38+cell proportion translated to a longer median progression-free survival (mPFS, 8.21 months vs 1.64 months, p=0.0065) and median overall survival (mOS, 19.06 months vs 9.59 months, p=0.0295). Patients with high CD38+CD68+macrophage density had a better mOS of 34.43 months compared with 9.66 months in patients with low CD38+CD68+ macrophage density. CD38hi macrophages produce more interferon γ (IFN-γ) and related cytokines, which may explain its predictive value when treated with ICB. Conclusions A high proportion of CD38+ cells, determined by IHC, predicts response to ICB and is associated with superior mPFS and OS in advanced HCC.
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Affiliation(s)
- Harry Ho Man Ng
- Duke-NUS Medical School, Singapore.,Division of Pathology, Singapore General Hospital, Singapore
| | - Ren Yuan Lee
- Division of Pathology, Singapore General Hospital, Singapore.,Nanyang Technological University, Singapore
| | - Siting Goh
- Division of Pathology, Singapore General Hospital, Singapore
| | | | - Xinru Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Valerie Chew
- Duke-NUS Medical School, Singapore.,SingHealth Translational Immunology and Inflammation Centre (STIIC), Singapore Health Services Pte Ltd, Singapore
| | - Huihua Li
- Division of Medicine, Singapore General Hospital, Singapore.,Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore
| | - Benedict Tan
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Sherlly Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Bijin Au
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | | | - Sahil Saraf
- Division of Pathology, Singapore General Hospital, Singapore
| | - John Edward Connolly
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Tracy Loh
- Division of Pathology, Singapore General Hospital, Singapore
| | - Wei Qiang Leow
- Division of Pathology, Singapore General Hospital, Singapore
| | | | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Fabio Malavasi
- Laboratory of Immunogenetics and CeRMS, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Ser Yee Lee
- Duke-NUS Medical School, Singapore.,Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital, Singapore
| | - Pierce Chow
- Duke-NUS Medical School, Singapore.,Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore
| | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - David Tai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Joe Yeong
- Division of Pathology, Singapore General Hospital, Singapore .,Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore.,Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore
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Chiu DKC, Yuen VWH, Cheu JWS, Wei LL, Ting V, Fehlings M, Sumatoh H, Nardin A, Newell EW, Ng IOL, Yau TCC, Wong CM, Wong CCL. Hepatocellular Carcinoma Cells Up-regulate PVRL1, Stabilizing PVR and Inhibiting the Cytotoxic T-Cell Response via TIGIT to Mediate Tumor Resistance to PD1 Inhibitors in Mice. Gastroenterology 2020; 159:609-623. [PMID: 32275969 DOI: 10.1053/j.gastro.2020.03.074] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 03/25/2020] [Accepted: 03/29/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Immune checkpoint inhibitors are effective in the treatment of some hepatocellular carcinomas (HCCs), but these tumors do not always respond to inhibitors of programmed cell death 1 (PDCD1, also called PD1). We investigated mechanisms of resistance of liver tumors in mice to infiltrating T cells. METHODS Mice were given hydrodynamic tail vein injections of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) and transposon vectors to disrupt Trp53 and overexpress C-Myc (Trp53KO/C-MycOE mice). Pvrl1 and Pvrl3 were knocked down in Hepa1-6 cells by using short hairpin RNAs. Hepa1-6 cells were injected into livers of C57BL/6 mice; some mice were given intraperitoneal injections of antibodies against PD1, T-cell immunoreceptor with Ig and ITIM domains (TIGIT), or CD8 before the cancer cells were injected. Liver tissues were collected from mice and analyzed by histology, immunohistochemistry, and quantitative real-time polymerase chain reaction; tumors were analyzed by mass cytometry using markers to detect T cells and other lymphocytes. We obtained HCC and nontumorous liver tissues and clinical data from patients who underwent surgery in Hong Kong and analyzed the tissues by immunohistochemistry. RESULTS Trp53KO/C-MycOE mice developed liver tumors in 3-5 weeks; injections of anti-PD1 did not slow tumor development. Tumors from mice given anti-PD1 had larger numbers of memory CD8+ T cells (CD44+CD62L-KLRG1int) and T cells that expressed PD1, lymphocyte activating 3 (LAG3), and TIGIT compared with mice not given the antibody. HCC tissues from patients had higher levels of PVRL1 messenger RNA and protein than nontumorous tissues. Increased PVRL1 was associated with shorter times of disease-free survival. Knockdown of Pvrl1 in Hepa1-6 cells caused them to form smaller tumors in mice, infiltrated by higher numbers of CD8+ T cells that expressed the inhibitory protein TIGIT; these effects were not observed in mice with depletion of CD8+ T cells. In Hepa1-6 cells, PVRL1 stabilized cell surface PVR, which interacted with TIGIT on CD8+ T cells; knockdown of Pvrl1 reduced cell-surface levels of PVR but not levels of Pvr messenger RNA. In Trp53KO/C-MycOE mice and mice with tumors grown from Hepa1-6 cells, injection of the combination of anti-PD1 and anti-TIGIT significantly reduced tumor growth, increased the ratio of cytotoxic to regulatory T cells in tumors, and prolonged survival. CONCLUSIONS PVRL1, which is up-regulated by HCC cells, stabilizes cell surface PVR, which interacts with TIGIT, an inhibitory molecule on CD8+ effector memory T cells. This suppresses the ant-tumor immune response. Inhibitors of PVRL1/TIGIT, along with anti-PD1 might be developed for treatment of HCC.
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Affiliation(s)
| | | | | | - Larry Lai Wei
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Vox Ting
- Department of Medicine, The University of Hong Kong, Hong Kong
| | | | | | | | - Evan W Newell
- ImmunoSCAPE Pte Ltd, Singapore; Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Thomas Chung-Cheung Yau
- Department of Medicine, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Carmen Chak-Lui Wong
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong.
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35
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Le Bert N, Gill US, Hong M, Kunasegaran K, Tan DZM, Ahmad R, Cheng Y, Dutertre CA, Heinecke A, Rivino L, Tan A, Hansi NK, Zhang M, Xi S, Chong Y, Pflanz S, Newell EW, Kennedy PTF, Bertoletti A. Effects of Hepatitis B Surface Antigen on Virus-Specific and Global T Cells in Patients With Chronic Hepatitis B Virus infection. Gastroenterology 2020; 159:652-664. [PMID: 32302614 DOI: 10.1053/j.gastro.2020.04.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Chronic hepatitis B virus (HBV) infection is characterized by the presence of defective viral envelope proteins (hepatitis B surface antigen [HBsAg]) and the duration of infection-most patients acquire the infection at birth or during the first years of life. We investigated the effects of these factors on patients' lymphocyte and HBV-specific T-cell populations. METHODS We collected blood samples and clinical data from 243 patients with HBV infection (3-75 years old) in the United Kingdom and China. We measured levels of HBV DNA, HBsAg, hepatitis B e antigen, and alanine aminotransferase; analyzed HBV genotypes; and isolated peripheral blood mononuclear cells (PBMCs). In PBMCs from 48 patients with varying levels of serum HBsAg, we measured 40 markers on nature killer and T cells by mass cytometry. PBMCs from 189 patients with chronic infection and 38 patients with resolved infections were incubated with HBV peptide libraries, and HBV-specific T cells were identified by interferon gamma enzyme-linked immune absorbent spot (ELISpot) assays or flow cytometry. We used multivariate linear regression and performed variable selection using the Akaike information criterion to identify covariates associated with HBV-specific responses of T cells. RESULTS Although T- and natural killer cell phenotypes and functions did not change with level of serum HBsAg, numbers of HBs-specific T cells correlated with serum levels of HBsAg (r = 0.3367; P < .00001). After we performed the variable selection, the multivariate linear regression model identified patient age as the only factor significantly associated with numbers of HBs-specific T cells (P = .000115). In patients younger than 30 years, HBs-specific T cells constituted 28.26% of the total HBV-specific T cells; this value decreased to 7.14% in patients older than 30 years. CONCLUSIONS In an analysis of immune cells from patients with chronic HBV infection, we found that the duration of HBsAg exposure, rather than the quantity of HBsAg, was associated with the level of anti-HBV immune response. Although the presence of HBs-specific T cells might not be required for the clearance of HBV infection in all patients, strategies to restore anti-HBV immune responses should be considered in patients younger than 30 years.
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Affiliation(s)
- Nina Le Bert
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Upkar S Gill
- Barts Liver Centre, Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Michelle Hong
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Kamini Kunasegaran
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Damien Z M Tan
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Raidah Ahmad
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Yang Cheng
- Singapore Immunology Network, A∗STAR, Singapore
| | - Charles-A Dutertre
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore; Singapore Immunology Network, A∗STAR, Singapore
| | | | - Laura Rivino
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore; School of Cellular and Molecular Medicine, University of Bristol, United Kingdom
| | - Anthony Tan
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Navjyot K Hansi
- Barts Liver Centre, Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Min Zhang
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sujuan Xi
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yutian Chong
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Stefan Pflanz
- Gilead Sciences, Inc, Department of Biology, Foster City, California
| | | | - Patrick T F Kennedy
- Barts Liver Centre, Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore; Singapore Immunology Network, A∗STAR, Singapore.
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Kwok I, Becht E, Xia Y, Ng M, Teh YC, Tan L, Evrard M, Li JLY, Tran HTN, Tan Y, Liu D, Mishra A, Liong KH, Leong K, Zhang Y, Olsson A, Mantri CK, Shyamsunder P, Liu Z, Piot C, Dutertre CA, Cheng H, Bari S, Ang N, Biswas SK, Koeffler HP, Tey HL, Larbi A, Su IH, Lee B, St John A, Chan JKY, Hwang WYK, Chen J, Salomonis N, Chong SZ, Grimes HL, Liu B, Hidalgo A, Newell EW, Cheng T, Ginhoux F, Ng LG. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Immunity 2020; 53:303-318.e5. [PMID: 32579887 DOI: 10.1016/j.immuni.2020.06.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/14/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
Granulocyte-monocyte progenitors (GMPs) have been previously defined for their potential to generate various myeloid progenies such as neutrophils and monocytes. Although studies have proposed lineage heterogeneity within GMPs, it is unclear if committed progenitors already exist among these progenitors and how they may behave differently during inflammation. By combining single-cell transcriptomic and proteomic analyses, we identified the early committed progenitor within the GMPs responsible for the strict production of neutrophils, which we designate as proNeu1. Our dissection of the GMP hierarchy led us to further identify a previously unknown intermediate proNeu2 population. Similar populations could be detected in human samples. proNeu1s, but not proNeu2s, selectively expanded during the early phase of sepsis at the expense of monocytes. Collectively, our findings help shape the neutrophil maturation trajectory roadmap and challenge the current definition of GMPs.
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Affiliation(s)
- Immanuel Kwok
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Etienne Becht
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yu Xia
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Melissa Ng
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Jackson L Y Li
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Hoa T N Tran
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore
| | - Dehua Liu
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Archita Mishra
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ka Hang Liong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Keith Leong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yuning Zhang
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Chinmay Kumar Mantri
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Cecile Piot
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Sudipto Bari
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Nicholas Ang
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Subhra K Biswas
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - H Philip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA 90048, USA; Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore 119074, Singapore
| | - Hong Liang Tey
- National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - I-Hsin Su
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ashley St John
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA; SingHealth Duke-National University of Singapore Global Health Institute, Singapore 168753, Singapore
| | - Jerry K Y Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - William Y K Hwang
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; National Cancer Centre Singapore, Singapore 169610, Singapore; Department of Hematology, Singapore General Hospital, Singapore 169608, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; National Cancer Centre Singapore, Singapore 169610, Singapore.
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Chua KLM, Fehlings M, Yeo ELL, Nardin A, Sumatoh H, Chu PL, Nei WL, Ong EHW, Woo WY, Low KP, Wang H, Poon DJJ, Liang ZG, Yao K, Huang L, Toh CK, Ang MK, Farid M, Cheng XM, Kanesvaran R, Dent R, Wee JTS, Lim TKH, Iyer NG, Tan DSW, Soo KC, Newell EW, Chua MLK. High-Dimensional Characterization of the Systemic Immune Landscape Informs on Synergism Between Radiation Therapy and Immune Checkpoint Blockade. Int J Radiat Oncol Biol Phys 2020; 108:70-80. [PMID: 32544576 DOI: 10.1016/j.ijrobp.2020.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Improved antitumor responses have been observed in patients after combination radiation therapy (RT) and immune checkpoint blockade (ICB). Whether these clinical responses are linked to the host systemic immune system has not been elucidated. METHODS AND MATERIALS In this single-institution prospective observational study, peripheral blood was longitudinally collected from 10 patients with metastatic disease who had responded to anti-PD-1/anti-PD-L1 ICB and received RT (8-50 Gy in 1-5 fractions) upon disease progression at the following timepoints: baseline (pre-RT), 1 to 2 weeks post-RT, and post-ICB (cycle 1) on reintroduction post-RT. To thoroughly characterize the interaction between combined RT-ICB and the host immune system, we performed high-dimensional, mass cytometry-based immunophenotyping of circulating lymphocytes using a 40-marker panel addressing lineage, differentiation, activation, trafficking, cytotoxicity, and costimulatory and inhibitory functions. Phenotypic expression of circulating lymphocytes was compared across patients and time points and correlated with post-RT tumor responses. RESULTS Foremost, we demonstrated excellent posttreatment clinical responses, including 4 local responses with >50% reduction in radiated tumor size, 1 out-of-field response, and 4 patients who resumed ICB for >1 year. Baseline and post-RT immune states were highly heterogeneous among patients. Despite this interindividual heterogeneity in baseline immune states, we observed a systemic immune reaction to RT-ICB common across patients, histology, and radiation sites; a subset of pre-existing Ki-67+ CD8+ T cells were increased post-RT and further expanded upon reintroduction of ICB post-RT (2.3-fold increase, P = .02). Importantly, RT did not alter the phenotypic profile of these Ki-67+ CD8+ T cells, which was characterized by a distinct activated and differentiated effector phenotype. CONCLUSIONS Collectively, these findings point toward a sustained reinvigoration of host antitumor immunity after RT-ICB and suggest an expansion in activated Ki-67+ CD8+ T cells as a possible demonstration of this synergy, thereby providing new insights that may support the development of optimal sequencing strategies.
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Affiliation(s)
- Kevin L M Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore; Oncology Academic Programme, Duke-NUS Medical School, Singapore
| | | | - Eugenia L L Yeo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | | | | | - Pek Lim Chu
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Wen-Long Nei
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore; Oncology Academic Programme, Duke-NUS Medical School, Singapore
| | - Enya H W Ong
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
| | - Wai Yee Woo
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
| | - Kar Perng Low
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Haitao Wang
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Dennis J J Poon
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore
| | - Zhong-Guo Liang
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Kai Yao
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Luo Huang
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing Cancer Hospital & Institute, Chongqing, People's Republic of China
| | - Chee Keong Toh
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Mei-Kim Ang
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Mohamad Farid
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Xin Min Cheng
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Ravindran Kanesvaran
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rebecca Dent
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Joseph T S Wee
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore; Oncology Academic Programme, Duke-NUS Medical School, Singapore
| | - Tony K H Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - N Gopalakrishna Iyer
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Daniel S W Tan
- Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Division of Medical Oncology, National Cancer Centre Singapore, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Khee Chee Soo
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore; Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Evan W Newell
- immunoSCAPE Pte Ltd; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Melvin L K Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore; Oncology Academic Programme, Duke-NUS Medical School, Singapore; Division of Medical Sciences, National Cancer Centre Singapore, Singapore.
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Mair F, Erickson JR, Voillet V, Simoni Y, Bi T, Tyznik AJ, Martin J, Gottardo R, Newell EW, Prlic M. A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level. Cell Rep 2020; 31:107499. [PMID: 32268080 PMCID: PMC7224638 DOI: 10.1016/j.celrep.2020.03.063] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 07/15/2019] [Revised: 10/31/2019] [Accepted: 03/18/2020] [Indexed: 12/30/2022] Open
Abstract
High-throughput single-cell RNA sequencing (scRNA-seq) has become a frequently used tool to assess immune cell heterogeneity. Recently, the combined measurement of RNA and protein expression was developed, commonly known as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcripts but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets. Here, we describe a targeted transcriptomics approach that combines an analysis of over 400 genes with simultaneous measurement of over 40 proteins on 2 × 104 cells in a single experiment. This targeted approach requires only about one-tenth of the read depth compared to a whole-transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic datasets, we adapted one-dimensional soli expression by nonlinear stochastic embedding (One-SENSE) for intuitive visualization of protein-transcript relationships on a single-cell level.
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Affiliation(s)
- Florian Mair
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Jami R Erickson
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Valentin Voillet
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Yannick Simoni
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Timothy Bi
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | | | | | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA.
| | - Evan W Newell
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA.
| | - Martin Prlic
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; Department of Global Health and Department of Immunology, University of Washington, Seattle, WA 98195, USA.
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Farrera C, Melchiotti R, Petrov N, Weng Teng KW, Wong MT, Loh CY, Villanova F, Tosi I, Chen J, Grys K, Sreeneebus H, Chapman A, Perera GK, Heck S, Gracio F, de Rinaldis E, Barker JN, Smith CH, Nestle FO, Newell EW, Di Meglio P. T-cell phenotyping uncovers systemic features of atopic dermatitis and psoriasis. J Allergy Clin Immunol 2020; 145:1021-1025.e15. [DOI: 10.1016/j.jaci.2019.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022]
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40
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Lai SM, Sheng J, Gupta P, Renia L, Duan K, Zolezzi F, Karjalainen K, Newell EW, Ruedl C. Organ-Specific Fate, Recruitment, and Refilling Dynamics of Tissue-Resident Macrophages during Blood-Stage Malaria. Cell Rep 2019; 25:3099-3109.e3. [PMID: 30540942 DOI: 10.1016/j.celrep.2018.11.059] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/14/2018] [Accepted: 11/14/2018] [Indexed: 12/31/2022] Open
Abstract
Inflammation-induced disappearance of tissue-resident macrophages represents a key pathogen defense mechanism. Using a model of systemic blood-stage malaria, we studied the dynamics of tissue-resident macrophages in multiple organs to determine how they are depleted and refilled during the course of disease. We show that Plasmodium infection results in a transient loss of embryonically established resident macrophages prior to the parasitemia peak. Fate-mapping analysis reveals that inflammatory monocytes contribute to the repopulation of the emptied niches of splenic red pulp macrophages and hepatic Kupffer cells, while lung alveolar macrophages refill their niche predominantly through self-renewal. Interestingly, the local microenvironment of the spleen and liver can "imprint" the molecular characteristics of fetal-derived macrophages on newly differentiated bone marrow-derived immigrants with remarkably similar gene expression profiles and turnover kinetics. Thus, the mononuclear phagocytic system has developed distinct but effective tissue-specific strategies to replenish emptied niches to guarantee the functional integrity of the system.
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Affiliation(s)
- Si Min Lai
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore; Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Jianpeng Sheng
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Pravesh Gupta
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Laurent Renia
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Kaibo Duan
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Klaus Karjalainen
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Evan W Newell
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Christiane Ruedl
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore.
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Chng MHY, Lim MQ, Rouers A, Becht E, Lee B, MacAry PA, Lye DC, Leo YS, Chen J, Fink K, Rivino L, Newell EW. Large-Scale HLA Tetramer Tracking of T Cells during Dengue Infection Reveals Broad Acute Activation and Differentiation into Two Memory Cell Fates. Immunity 2019; 51:1119-1135.e5. [PMID: 31757672 DOI: 10.1016/j.immuni.2019.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 08/01/2019] [Accepted: 10/21/2019] [Indexed: 12/25/2022]
Abstract
T cells play important multifaceted roles during dengue infection, and understanding their responses is important for defining correlates of protective immunity and identifying effective vaccine antigens. Using mass cytometry and a highly multiplexed peptide-HLA (human leukocyte antigen) tetramer staining strategy, we probed T cells from dengue patients-a total of 430 dengue and control candidate epitopes-together with key markers of activation, trafficking, and differentiation. During acute disease, dengue-specific CD8+ T cells expressed a distinct profile of activation and trafficking receptors that distinguished them from non-dengue-specific T cells. During convalescence, dengue-specific T cells differentiated into two major cell fates, CD57+ CD127--resembling terminally differentiated senescent memory cells and CD127+ CD57--resembling proliferation-capable memory cells. Validation in an independent cohort showed that these subsets remained at elevated frequencies up to one year after infection. These analyses aid our understanding of the generation of T cell memory in dengue infection or vaccination.
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Affiliation(s)
- Melissa Hui Yen Chng
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Mei Qiu Lim
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Angeline Rouers
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Etienne Becht
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Paul A MacAry
- Immunology Programme, Department of Microbiology and Immunology, Life Science Institute, National University of Singapore, Singapore 117456, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore 308442, Singapore; Tan Tock Seng Hospital, Singapore 308433, Singapore; Lee Kong Chian School of Medicine, Singapore 308232, Singapore; Yong Loo Lin School of Medicine, Singapore 119228, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore 308442, Singapore; Tan Tock Seng Hospital, Singapore 308433, Singapore; Lee Kong Chian School of Medicine, Singapore 308232, Singapore; Yong Loo Lin School of Medicine, Singapore 119228, Singapore; Saw Swee Hock School of Public Health, Singapore 117549, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Laura Rivino
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.
| | - Evan W Newell
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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42
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Claser C, Nguee SYT, Balachander A, Wu Howland S, Becht E, Gunasegaran B, Hartimath SV, Lee AWQ, Theng Theng Ho J, Bing Ong C, Newell EW, Goggi J, Guan Ng L, Renia L. Lung endothelial cell antigen cross-presentation to CD8 +T cells drives malaria-associated lung injury. Nat Commun 2019; 10:4241. [PMID: 31534124 PMCID: PMC6751193 DOI: 10.1038/s41467-019-12017-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 01/29/2019] [Accepted: 08/15/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria-associated acute respiratory distress syndrome (ARDS) and acute lung injury (ALI) are life-threatening manifestations of severe malaria infections. The pathogenic mechanisms that lead to respiratory complications, such as vascular leakage, remain unclear. Here, we confirm that depleting CD8+T cells with anti-CD8β antibodies in C57BL/6 mice infected with P. berghei ANKA (PbA) prevent pulmonary vascular leakage. When we transfer activated parasite-specific CD8+T cells into PbA-infected TCRβ-/- mice (devoid of all T-cell populations), pulmonary vascular leakage recapitulates. Additionally, we demonstrate that PbA-infected erythrocyte accumulation leads to lung endothelial cell cross-presentation of parasite antigen to CD8+T cells in an IFNγ-dependent manner. In conclusion, pulmonary vascular damage in ALI is a consequence of IFNγ-activated lung endothelial cells capturing, processing, and cross-presenting malaria parasite antigen to specific CD8+T cells induced during infection. The mechanistic understanding of the immunopathogenesis in malaria-associated ARDS and ALI provide the basis for development of adjunct treatments.
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Affiliation(s)
- Carla Claser
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore.
| | - Samantha Yee Teng Nguee
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2 Blk MD4, Level 3, Singapore, 117545, Singapore
| | - Akhila Balachander
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Shanshan Wu Howland
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Etienne Becht
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Bavani Gunasegaran
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Siddesh V Hartimath
- Isotopic Molecular Imaging Laboratory, Singapore Bioimaging Consortium (SBIC), A*STAR, 11 Biopolis Way, #02-02 Helios, Singapore, 138667, Singapore
| | - Audrey W Q Lee
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Jacqueline Theng Theng Ho
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Chee Bing Ong
- Histolopathology/Advanced Molecular Pathology Lab, Institute of Molecular and Cell Biology (IMCB), A*STAR, 61 Biopolis Drive, Level 6 Proteos Building, Singapore, 138673, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Julian Goggi
- Isotopic Molecular Imaging Laboratory, Singapore Bioimaging Consortium (SBIC), A*STAR, 11 Biopolis Way, #02-02 Helios, Singapore, 138667, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore
| | - Laurent Renia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Level 3 & 4 Immunos Building, Singapore, 138648, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2 Blk MD4, Level 3, Singapore, 117545, Singapore.
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43
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Fehlings M, Jhunjhunwala S, Kowanetz M, O'Gorman WE, Hegde PS, Sumatoh H, Lee BH, Nardin A, Becht E, Flynn S, Ballinger M, Newell EW, Yadav M. Late-differentiated effector neoantigen-specific CD8+ T cells are enriched in peripheral blood of non-small cell lung carcinoma patients responding to atezolizumab treatment. J Immunother Cancer 2019; 7:249. [PMID: 31511069 PMCID: PMC6740011 DOI: 10.1186/s40425-019-0695-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND There is strong evidence that immunotherapy-mediated tumor rejection can be driven by tumor-specific CD8+ T cells reinvigorated to recognize neoantigens derived from tumor somatic mutations. Thus, the frequencies or characteristics of tumor-reactive, mutation-specific CD8+ T cells could be used as biomarkers of an anti-tumor response. However, such neoantigen-specific T cells are difficult to reliably identify due to their low frequency in peripheral blood and wide range of potential epitope specificities. METHODS Peripheral blood mononuclear cells (PBMC) from 14 non-small cell lung cancer (NSCLC) patients were collected pre- and post-treatment with the anti-PD-L1 antibody atezolizumab. Using whole exome sequencing and RNA sequencing we identified tumor neoantigens that are predicted to bind to major histocompatibility complex class I (MHC-I) and utilized mass cytometry, together with cellular 'barcoding', to profile immune cells from patients with objective response to therapy (n = 8) and those with progressive disease (n = 6). In parallel, a highly-multiplexed combinatorial tetramer staining was used to screen antigen-specific CD8+ T cells in peripheral blood for 782 candidate tumor neoantigens and 71 known viral-derived control peptide epitopes across all patient samples. RESULTS No significant treatment- or response associated phenotypic difference were measured in bulk CD8+ T cells. Multiplexed peptide-MHC multimer staining detected 20 different neoantigen-specific T cell populations, as well as T cells specific for viral control antigens. Not only were neoantigen-specific T cells more frequently detected in responding patients, their phenotypes were also almost entirely distinct. Neoantigen-specific T cells from responder patients typically showed a differentiated effector phenotype, most like Cytomegalovirus (CMV) and some types of Epstein-Barr virus (EBV)-specific CD8+ T cells. In contrast, more memory-like phenotypic profiles were observed for neoantigen-specific CD8+ T cells from patients with progressive disease. CONCLUSION This study demonstrates that neoantigen-specific T cells can be detected in peripheral blood in non-small cell lung cancer (NSCLC) patients during anti-PD-L1 therapy. Patients with an objective response had an enrichment of neoantigen-reactive T cells and these cells showed a phenotype that differed from patients without a response. These findings suggest the ex vivo identification, characterization, and longitudinal follow-up of rare tumor-specific differentiated effector neoantigen-specific T cells may be useful in predicting response to checkpoint blockade. TRIAL REGISTRATION POPLAR trial NCT01903993 .
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Affiliation(s)
| | | | | | | | - Priti S Hegde
- Genentech, 1 DNA way, South San Francisco, CA, 94080, USA
| | | | | | | | - Etienne Becht
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore, Singapore
| | - Susan Flynn
- Genentech, 1 DNA way, South San Francisco, CA, 94080, USA
| | | | | | - Mahesh Yadav
- Genentech, 1 DNA way, South San Francisco, CA, 94080, USA.
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44
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Dress RJ, Dutertre CA, Giladi A, Schlitzer A, Low I, Shadan NB, Tay A, Lum J, Kairi MFBM, Hwang YY, Becht E, Cheng Y, Chevrier M, Larbi A, Newell EW, Amit I, Chen J, Ginhoux F. Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage. Nat Immunol 2019; 20:852-864. [DOI: 10.1038/s41590-019-0420-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 05/13/2019] [Indexed: 01/19/2023]
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45
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Cheng Y, Zhu YO, Becht E, Aw P, Chen J, Poidinger M, de Sessions PF, Hibberd ML, Bertoletti A, Lim SG, Newell EW. Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection. Sci Immunol 2019; 4:4/32/eaau6905. [DOI: 10.1126/sciimmunol.aau6905] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022]
Abstract
Associations between chronic antigen stimulation, T cell dysfunction, and the expression of various inhibitory receptors are well characterized in several mouse and human systems. During chronic hepatitis B virus (HBV) infection (CHB), T cell responses are blunted with low frequencies of virus-specific T cells observed, making these parameters difficult to study. Here, using mass cytometry and a highly multiplexed combinatorial peptide–major histocompatibility complex (pMHC) tetramer strategy that allows for the detection of rare antigen-specific T cells, we simultaneously probed 484 unique HLA-A*1101–restricted epitopes spanning the entire HBV genome on T cells from patients at various stages of CHB. Numerous HBV-specific T cell populations were detected, validated, and profiled. T cells specific for two epitopes (HBVpol387and HBVcore169) displayed differing and complex heterogeneities that were associated with the disease progression, and the expression of inhibitory receptors on these cells was not linearly related with their extent of T cell dysfunction. For HBVcore169-specific CD8+T cells, we found cellular markers associated with long-term memory, polyfunctionality, and the presence of several previously unidentified public TCR clones that correlated with viral control. Using high-dimensional trajectory analysis of these cellular phenotypes, a pseudo-time metric was constructed that fit with the status of viral infection in corresponding patients. This was validated in a longitudinal cohort of patients undergoing antiviral therapy. Our study uncovers complex relationships of inhibitory receptors between the profiles of antigen-specific T cells and the status of CHB with implications for new strategies of therapeutic intervention.
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46
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Yeong J, Lim JCT, Lee B, Li H, Ong CCH, Thike AA, Yeap WH, Yang Y, Lim AYH, Tay TKY, Liu J, Wong SC, Chen J, Lim EH, Iqbal J, Dent R, Newell EW, Tan PH. Prognostic value of CD8 + PD-1+ immune infiltrates and PDCD1 gene expression in triple negative breast cancer. J Immunother Cancer 2019; 7:34. [PMID: 30728081 PMCID: PMC6366051 DOI: 10.1186/s40425-019-0499-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
The role of programmed cell death protein-1 (PD-1)/programmed cell death ligand 1 (PD-L1) in triple negative breast cancer (TNBC) remains to be fully understood. In this study, we investigated the role of PD-1 as a prognostic marker for TNBC in an Asian cohort (n = 269). Samples from patients with TNBC were labeled with antibodies against PD-L1 and PD-1, and subjected to NanoString assays to measure the expression of immune-related genes. Associations between disease-free survival (DFS), overall survival (OS) and biomarker expression were investigated. Multivariate analysis showed that tumors with high PD-1+ immune infiltrates harbored significantly increased DFS, and this increase was significant even after controlling for clinicopathological parameters (HR 0.95; P = 0.030). In addition, the density of cells expressing both CD8 and PD-1, but not the density of CD8−PD-1+ immune infiltrates, was associated with improved DFS. Notably, this prognostic significance was independent of clinicopathological parameters and the densities of total CD8+ cell (HR 0.43, P = 0.011). At the transcriptional level, high expression of PDCD1 within the tumor was significantly associated with improved DFS (HR 0.38; P = 0.027). In line with these findings, high expression of IFNG (HR 0.38; P = 0.001) and IFN signaling genes (HR 0.46; p = 0.027) was also associated with favorable DFS. Inclusion of PD-1 immune infiltrates and PDCD1 gene expression added significant prognostic value for DFS (ΔLRχ2 = 6.35; P = 0.041) and OS (ΔLRχ2 = 9.53; P = 0.008), beyond that provided by classical clinicopathological variables. Thus, PD-1 mRNA and protein expression status represent a promising, independent indicator of prognosis in TNBC.
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Affiliation(s)
- Joe Yeong
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore.,Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Jeffrey Chun Tatt Lim
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Huihua Li
- Division of Medicine, Singapore General Hospital, Singapore, Singapore
| | - Clara Chong Hui Ong
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore
| | - Aye Aye Thike
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Wei Hseun Yeap
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Yi Yang
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore.,Shanghai University of Finance and Economics, Shanghai, China
| | - Ansel Yi Herh Lim
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Timothy Kwang Yong Tay
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Siew-Cheng Wong
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Elaine Hsuen Lim
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Jabed Iqbal
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Rebecca Dent
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A, Biomedical Grove, Immunos, Singapore, 138648, Singapore.
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore. .,Duke-NUS Medical School, Singapore, Singapore.
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47
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Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ. Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity 2019; 48:1029-1045.e5. [PMID: 29768164 DOI: 10.1016/j.immuni.2018.04.026] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 02/14/2018] [Accepted: 04/24/2018] [Indexed: 01/30/2023]
Abstract
Exhausted CD8 T (Tex) cells are immunotherapy targets in chronic infection and cancer, but a comprehensive assessment of Tex cell diversity in human disease is lacking. Here, we developed a transcriptomic- and epigenetic-guided mass cytometry approach to define core exhaustion-specific genes and disease-induced changes in Tex cells in HIV and human cancer. Single-cell proteomic profiling identified 9 distinct Tex cell clusters using phenotypic, functional, transcription factor, and inhibitory receptor co-expression patterns. An exhaustion severity metric was developed and integrated with high-dimensional phenotypes to define Tex cell clusters that were present in healthy subjects, common across chronic infection and cancer or enriched in either disease, linked to disease severity, and changed with HIV therapy. Combinatorial patterns of immunotherapy targets on different Tex cell clusters were also defined. This approach and associated datasets present a resource for investigating human Tex cell biology, with implications for immune monitoring and immunomodulation in chronic infections, autoimmunity, and cancer.
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Affiliation(s)
- Bertram Bengsch
- Department of Microbiology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Department of Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Freiburg, Germany.
| | - Takuya Ohtani
- Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Omar Khan
- Department of Microbiology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Manu Setty
- Program for Computational and Systems Biology, Sloan Kettering Institute, New York, NY, USA
| | - Sasikanth Manne
- Department of Microbiology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Shaun O'Brien
- Department of Medicine, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | | | - Ramin Sedaghat Herati
- Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Department of Medicine, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Department of Medicine, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Kyong-Mi Chang
- Department of Medicine, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, PA, USA
| | - Evan W Newell
- Agency for Science, Technology and Research, Singapore Immunology Network, Singapore
| | - Niels Bovenschen
- Department of Pathology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, New York, NY, USA
| | - Steven M Albelda
- Department of Medicine, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Department of Microbiology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA.
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48
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Affiliation(s)
- Étienne Becht
- Singapore Immunology Network (SIgN), Agency for science, technology and research, 8A Biomedical Grove, 138648 Singapour
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for science, technology and research, 8A Biomedical Grove, 138648 Singapour
| | - Yannick Simoni
- Singapore Immunology Network (SIgN), Agency for science, technology and research, 8A Biomedical Grove, 138648 Singapour
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49
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Abstract
Antigen-specific CD8+ T cells play a crucial role in the host protective immune response against viruses, tumors, and other diseases. Major histocompatibility complex (MHC) class I tetramers allow for a direct detection of such antigen-specific CD8+ T cells. Using mass cytometry together with multiplex MHC class I tetramer staining, we are able to screen more than 1000 different antigen candidates simultaneously across tissues in health and disease, while retaining the possibility to deliver an in-depth characterization of antigen-specific CD8+ T cells and associated phenotypes. Here we describe the method for a MHC class I tetramer multiplexing approach together with intracellular antibody staining for a parallel phenotypic cell characterization using mass cytometry in human specimens.
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Affiliation(s)
- Yannick Simoni
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore, Singapore. .,Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
| | | | - Evan W Newell
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore, Singapore. .,Fred Hutch Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
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50
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Becht E, McInnes L, Healy J, Dutertre CA, Kwok IWH, Ng LG, Ginhoux F, Newell EW. Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol 2018; 37:nbt.4314. [PMID: 30531897 DOI: 10.1038/nbt.4314] [Citation(s) in RCA: 2156] [Impact Index Per Article: 359.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023]
Abstract
Advances in single-cell technologies have enabled high-resolution dissection of tissue composition. Several tools for dimensionality reduction are available to analyze the large number of parameters generated in single-cell studies. Recently, a nonlinear dimensionality-reduction technique, uniform manifold approximation and projection (UMAP), was developed for the analysis of any type of high-dimensional data. Here we apply it to biological data, using three well-characterized mass cytometry and single-cell RNA sequencing datasets. Comparing the performance of UMAP with five other tools, we find that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters. The work highlights the use of UMAP for improved visualization and interpretation of single-cell data.
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Affiliation(s)
- Etienne Becht
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Leland McInnes
- Tutte Institute for Mathematics and Computing, Ottawa, Ontario, Canada
| | - John Healy
- Tutte Institute for Mathematics and Computing, Ottawa, Ontario, Canada
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Immanuel W H Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
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