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Keenan BP, McCarthy EE, Ilano A, Yang H, Zhang L, Allaire K, Fan Z, Li T, Lee DS, Sun Y, Cheung A, Luong D, Chang H, Chen B, Marquez J, Sheldon B, Kelley RK, Ye CJ, Fong L. Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis. Cell Rep 2022; 40:111384. [PMID: 36130508 PMCID: PMC10060099 DOI: 10.1016/j.celrep.2022.111384] [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: 12/01/2021] [Revised: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 01/17/2023] Open
Abstract
Suppressive myeloid cells can contribute to immunotherapy resistance, but their role in response to checkpoint inhibition (CPI) in anti-PD-1 refractory cancers, such as biliary tract cancer (BTC), remains elusive. We use multiplexed single-cell transcriptomic and epitope sequencing to profile greater than 200,000 peripheral blood mononuclear cells from advanced BTC patients (n = 9) and matched healthy donors (n = 8). Following anti-PD-1 treatment, CD14+ monocytes expressing high levels of immunosuppressive cytokines and chemotactic molecules (CD14CTX) increase in the circulation of patients with BTC tumors that are CPI resistant. CD14CTX can directly suppress CD4+ T cells and induce SOCS3 expression in CD4+ T cells, rendering them functionally unresponsive. The CD14CTX gene signature associates with worse survival in patients with BTC as well as in other anti-PD-1 refractory cancers. These results demonstrate that monocytes arising after anti-PD-1 treatment can induce T cell paralysis as a distinct mode of tumor-mediated immunosuppression leading to CPI resistance.
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Affiliation(s)
- Bridget P Keenan
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth E McCarthy
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Arielle Ilano
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hai Yang
- Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Li Zhang
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Kathryn Allaire
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Zenghua Fan
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David S Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander Cheung
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diamond Luong
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hewitt Chang
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Brandon Chen
- Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jaqueline Marquez
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA
| | - Brenna Sheldon
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robin K Kelley
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chun Jimmie Ye
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; J. David Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Lawrence Fong
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA, USA; Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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Keenan B, McCarthy E, Ilano A, Yang H, Zhang L, Allaire K, Fan Z, Li T, Lee D, Sun Y, Cheung A, Chang H, Sheldon B, Kelley R, Ye CJ, Fong L. 676 Altered circulating myeloid states associated with anti-PD-1 resistance induce T cell paralysis in human biliary cancer. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundAdvanced biliary cancers (ABC) have a poor prognosis and low rates of response to immune checkpoint inhibition (CPI), with overall response rates ranging from 3–13%.1–3 Although suppressive myeloid cells have been proposed as a mechanism of resistance to immunotherapy in general, their relationship to response to CPI is unknown.MethodsWe used multiplexed simultaneous single cell RNA sequencing and cell surface proteomics (CITE-seq) to profile circulating immune cells in ABC patients receiving anti-PD-1 at longitudinal timepoints pre-immunotherapy and on treatment, as well as from healthy donors. We also performed single cell RNA sequencing on resected biliary tumors.ResultsWe identified a novel population of circulating cancer-enriched myeloid cells (CEM) characterized by chemokines and extracellular matrix digestion-related gene expression, which were present pre-treatment. Anti-PD-1 treatment drove the CEMs into two diverging states that were associated with response or resistance to treatment. CEM induced in non-responders constituted over 40% of the circulating myeloid cells and expressed immunosuppressive programs, including the upregulation of suppressive cytokines and chemokines. The frequency of these myeloid cells were correlated with the abundance of SOCS3-expressing CD4+ T cells. These SOCS3+CD4+ T cells also colocalized with tumor-infiltrating myeloid cells that share CEM gene expression signatures in the biliary cancer microenvironment. Moreover, CEM can directly induce SOCS3-expressing T cells, which despite their naïve phenotype are functionally unresponsive. Finally, expression signatures of CEM and of SOCS3+CD4+ T cells are associated with worse survival in a larger cohort of ABC patients.ConclusionsThese results demonstrate the capacity of CEM to induce T cell paralysis as an alternate mode of tumor-mediated immunosuppression. A deeper understanding of immune cell biology in ABC provides insights for developing novel therapeutics that can overcome immunotherapy resistance in biliary cancer as well as other tumor types.Trial RegistrationNCT02703714ReferencesUeno M, et al. Nivolumab alone or in combination with cisplatin plus gemcitabine in Japanese patients with unresectable or recurrent biliary tract cancer: a non-randomised, multicentre, open-label, phase 1 study. Lancet Gastroenterol Hepatol 2019;4:611–621.Piha-Paul SA, et al. Efficacy and safety of pembrolizumab for the treatment of advanced biliary cancer: results from the KEYNOTE-158 and KEYNOTE-028 studies. Int J Cancer 2020.Kim RD, et al. A Phase 2 Multi-institutional study of nivolumab for patients with advanced refractory biliary tract cancer. JAMA Oncol 2020;6:888–894.Ethics ApprovalInformed consent was obtained from all patients for participation in the listed trial and for use of blood and tumor samples in research studies.
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Keenan BP, Tamaki W, Liu E, Chen B, Cheung A, Gordan JD, Sheldon B, Zhang L, Kelley RK, Fong L. Abstract 4063: Single cell immune profiling of patients with advanced biliary cancers treated with combination checkpoint inhibition and GM-CSF reveals diverse T cell and myeloid cell mechanisms of action. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4063] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Advanced biliary cancers (ABC) including cholangiocarcinoma and gallbladder adenocarcinoma are rising in incidence with limited standard treatment options. While checkpoint inhibition (CPI) achieves durable tumor responses in subsets of patients across many malignancies, less than 10% of ABC patients respond to single agent PD-1-targeted therapy. Combination immunotherapy aims to overcome pre-existing and adaptive resistance to immunotherapy. GM-CSF is a cytokine that activates and matures antigen-presenting cells, suggesting the potential to enhance immune responses. The exact mechanisms of action of this cytokine have not been defined in cancer patients. The combination of GM-CSF and anti-CTLA-4 CPI demonstrated safety along with inducing clinical responses in melanoma and prostate cancer. We conducted a phase II trial of the novel combination of GM-CSF and pembrolizumab (Pembro) in patients with ABC which has resulted in durable clinical responses in greater proportion than previously reported with anti-PD-1 monotherapy.
Methods: We assessed peripheral blood mononuclear cells (PBMC) from patients on Pembro monotherapy and combined Pembro/GM-CSF by mass cytometry (CyTOF) and T cell receptor (TCR) sequencing. We explored for the differences between clinical responders versus non-responders.
Results: We find that the addition of GM-CSF to Pembro leads to a higher frequency of myeloid cells overall; however, certain sub-populations of classical monocytes and conventional dendritic cells decreased in peripheral blood following upfront Pembro followed by GM-CSF. GM-CSF did not seem to change the phenotypes or relative frequencies of circulating T cell subsets. We also find that clinical responders possess specific circulating populations of classical monocyte and conventional dendritic cells prior to treatment. Responders also had higher percentages of CD8+ T cells expressing CD39 following Pembro treatment compared to non-responders. Combination therapy with Pembro/GM-CSF led to different effects on the T cell repertoire compared to Pembro alone.
Conclusions: The addition of GM-CSF to Pembro leads to dynamic shifts in myeloid cell subsets in the peripheral blood of ABC patients treated with immunotherapy, whereas Pembro alone led to changes in the activation states of T cell subsets. The TCR repertoire shifts reflect distinct mechanisms of action for Pembro monotherapy versus Pembro/GM-CSF. Future studies will explore the mechanisms driving the increased response rate seen with combination immunotherapy in comparison to Pembro alone in ABC patients, both through the study of peripheral immune responses as well as via immune-profiling of tumors from sequential biopsies of patients on Pembro monotherapy versus combined Pembro/GM-CSF.
Citation Format: Bridget P. Keenan, Whitney Tamaki, Eric Liu, Brandon Chen, Alexander Cheung, John D. Gordan, Brenna Sheldon, Li Zhang, Robin K. Kelley, Lawrence Fong. Single cell immune profiling of patients with advanced biliary cancers treated with combination checkpoint inhibition and GM-CSF reveals diverse T cell and myeloid cell mechanisms of action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4063.
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Affiliation(s)
| | - Whitney Tamaki
- University of California San Francisco, San Francisco, CA
| | - Eric Liu
- University of California San Francisco, San Francisco, CA
| | - Brandon Chen
- University of California San Francisco, San Francisco, CA
| | | | - John D. Gordan
- University of California San Francisco, San Francisco, CA
| | - Brenna Sheldon
- University of California San Francisco, San Francisco, CA
| | - Li Zhang
- University of California San Francisco, San Francisco, CA
| | | | - Lawrence Fong
- University of California San Francisco, San Francisco, CA
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